<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>Just to add to Daniels comments.</div><div><br></div><div>Things to change in step 1:</div><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><div>protein= <just try and add more protein evidence in general></div><div>est2genome=0</div><div>protein2genome=1</div><div>split_hit=20000</div><div>min_contig=50000</div></blockquote><div><br></div><div>Reasoning:</div><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><div>Your ESTs are very short especially if this is a lamprey species which have very long introns and really short exons. In lamprey (i.e. Petromyzon marinus), genes tend to be very long (remember gene lengths include introns and UTR and is not just the size of the coding sequence), so contigs shorter than 50kb are useless for training as you are unlikely to get nice complete gene models on those. Also lampreys have very long introns, so you have to allow for bigger introns in alignments (split_hit parameter). Finally add as much protein evidence from as many sources as possible. Your maker training run will take a long time as proteins take forever to align, but because of the evolutionary distance of lamprey from everything else and the short exon structure of its genome, very little aligns directly to its genome from other deuterstome and vertebrate species. I'm assuming this is a lamprey species because of what you said about the augustus species file you are using. Really the only thing closely related to lampreys unfortunately are other lampreys. Lancelets, hagfish, and sharks are not closely related to lamprey (while they branch closely together on the tree of life, there are too many years since the last common ancestor). So while they may have similar issues related to annotation (long introns and short exons etc.) they will not really match that well for the gene predictor or even protein alignments.</div></blockquote><div><br></div><div>Additional note:</div><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><div>I have training files for the lamprey species Petromyzon marinus for both Augustus and SNAP that I could share with you in a few week, when the genome publication is is released. But before that happens, new gene models will be available through the UCSC browser (hopefully within a couple of weeks), and gene models are already available through ENSEMBL. Get those protein files for training, it may be a big help for you. If you want early access to the lamprey training files for Augustus and SNAP, you would have to request it from Weiming Li at Michigan State University (the head of that genome project).</div><div><br></div></blockquote><div><br></div><div><br></div><div>Things to change in step 2:</div><blockquote style="margin:0 0 0 40px; border:none; padding:0px;">Optimally you would be doing de novo training using mRNAseq results, but with on;ly sparse protein alignments and such a fragmented assembly, you are probably better off just trying to adapt the human HMM files. They won't match that well, but you probably won't have the evidence for De Novo training. First make a copy of the augustus human species directory and rename it to lamprey (cp -R …/augustus/config/species/human …/augustus/config/species/lamprey). Use it as the base species for retraining augustus using your new models. You will have to edit multiple files in the directory after you copy it so that they no longer say human or homo sapiens internally or in the file name. Use maker2zff to generate the filtered ZFF file for training SNAP, but don't train SNAP. Rather use the training file to better train Augustus info here (just ignore the CEGMA part) --> <a href="http://sourceforge.net/mailarchive/message.php?msg_id=29361270">http://sourceforge.net/mailarchive/message.php?msg_id=29361270</a></blockquote><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><div><br></div><div>MAKE a backup of the step 1 maker output directory and run step 2 in the old step 1 directory (this allows you to change the parameters and reuse files form step 1 so you don't have to recalculate all the protein and EST alignments). So control files for step 2 are identical to step 1 except for these parameters.</div><div><br></div><div><div>protein2genome=0</div><div>augustus_species=lamprey</div><div>snaphmm=lamprey.hmm #optional if you decide to use SNAP</div></div><div><br></div><div>Don't both training SNAP here as you probably won't have enough data and you assembly is too fragmented for it to work well, so just stick to augustus. Try SNAP if you want just to see how well it works. Manually open up the largest contigs in a viewer to look at the models produced from the MAKER run to see if they look reasonable (this will also help you decide whether to keep SNAP).</div><div><br></div></blockquote><div><br></div><div>Things to change in step 3:</div><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><div>Step 3 should just be a clone of step 2 as it is bootstrapping. But make copies of …/augustus/config/species/lamprey and save it to …/augustus/config/species/lamprey2 (editing all the files and names as you did in step 2). This way you don't loose that training data if you decide to step back. Also Give your SNAP HMM a new name (I.e. lamprey2.hmm)</div></blockquote><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><div><br></div></blockquote><div><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><div>augustus_species=lamprey2</div><div>snaphmm=lamprey2.hmm #optional if you decide to use SNAP</div><div><br></div><div>Make a backup of Step 2 and run step 3 in the old Step 2 directory (This is for file reuse, so the step will run fast). This must be the exact same step directory as step 2 for the reuse trick to work.</div><div><br></div><div>Manually review the models and if you are satisfied move to step 4. Also note that most parameters including the protein, EST, and repeats should not change from step1-step3, and should not be removed for step 4 either, you can add more evidence, but don't remove evidence (like the repeats).</div><div><br></div><div><br></div></blockquote><div>Things to change in step 4:</div><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><div>For this step, just set min_contig=10000 and rerun MAKER inside the step 3 directory to get the smaller contigs annotated. This should be your final step, although you can try altering other parameters or adding more evidence sources here etc. </div></blockquote><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><div><br></div><div><br></div></blockquote><div>For other things to keep in mind, you should consider taking extra time to build a comprehensive library of repeats for your species, I know that Petromyzon marinus was virtually unannotatable until we had a very deep repeat library built for it. Any repeat library should be used in all steps. Also for lamprey, you will expect between 20,000-30,000 genes both because of your assemblies fragmentation and because of some ancestral genome duplication. Also be aware that lampreys appear to undergo programmed genome loss in somatic tissues, so any gene count you get is only going to represent a maximum of 75-80% of all genes unless the assembly is derived from germline tissue.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><div><br></div></blockquote></div><div>On 12-12-06 2:17 PM, "Daniel Ence" <<a href="mailto:dence@genetics.utah.edu">dence@genetics.utah.edu</a>> wrote:</div><div><br></div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>Hi Parul, </div><div><br></div><div>In step one, if protein2genome isn't turned on, then the protein alignments wont be used to generate gene models. Carson said before to use protein2genome to generate gene models for your trainings set, but you should know that those data aren't being used right now. </div><div><br></div><div>In step 2, you can include the est and protein evidence that you used in step one, and the ab-initio predictors will takes those data as hints to guide their predictions. Also, are you reannotating human here? I'm just wondering why the snap file is called Pult, but the augustus species model is human. Also, I think you should include the same masking files from step 1, otherwise the ab-initio predictors will be predicting on the unmasked sequence which will give you many spurious predictions. </div><div><br></div><div>In step 3, I'm not certain what you mean by boot-strapping. The control file you sent for step 3 will just pass-through all of the data from before. </div><div><br></div><div>In step 4, I think what you'll get is pretty close to what you already had in step 3. The gene models from step 3 are already based on the est and protein data from step 1, so without giving any different evidence or ab-initio predictors, I think that you will just get the same gene models that you got from step 3. Those gene models are what you should be using to train snap. Also, is this the same genome as in the other steps? The genome file here is called genome.linear.fa, but before it was called genome.fa.</div><div><br></div><div>Step 5. So maker uses both evidence and ab-initio predictions to create models. If you don't give any evidence (EST or protein) maker will not annotate any gene models. You have also changed the augustus species model in this step, but I don't know what you've gained by going from one species to another. You should be training augustus with the gene models and then creating a new species model in augustus. As I understand it, the filter only operates on gene models, not ab-initio predictions or alignments, so it probably isn't doing anything the way you have it set. </div><div><br></div><div>Step 6. I think step 5 and 6 should be combined. I don't know what you mean by boot-strapping here too. </div><div><br></div><div>Hopefully that clears up some of the confusion with how maker works. Carson will probably have a lot of suggestions too. </div><div><br></div><div>Thanks,</div><div>Daniel </div><div><br></div><div>Daniel Ence</div><div>Graduate Student</div><div>Eccles Institute of Human Genetics</div><div>University of Utah</div><div>15 North 2030 East, Room 2100</div><div>Salt Lake City, UT 84112-5330</div><div>________________________________________</div><div>From: Parul Kudtarkar [<a href="mailto:parulk@caltech.edu">parulk@caltech.edu</a>]</div><div>Sent: Thursday, December 06, 2012 10:08 AM</div><div>To: <a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a></div><div>Cc: Daniel Ence; <a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a></div><div>Subject: Re: [maker-devel] AED score</div><div><br></div><div>Hi Carson,</div><div><br></div><div>Once again thanks for a quick response. We expect to get 25,000 to 30,000</div><div>genes.</div><div>Here are the step</div><div>Step1. EST and proteins are used to predict gene-models. the resulting</div><div>file is used as training data-set for SNAP in step2. est2genome is turned</div><div>ON</div><div>Step2. Augustus and SNAP is used to predict genes.</div><div>Step3. The results are re-annoated(boot-strap)</div><div>Step4. EST and proteins are used to predict gene-models. The gff file from</div><div>step3. is used as model_gff. The resulting file is used as training</div><div>data-set for SNAP in step2</div><div>Step 5. Augustus and SNAP is used to predict genes. with AED set to 0.5</div><div>Step6. The results are re-annoated(boot-strap) with AED set to 0.5 and</div><div>contig_size to 10kb</div><div><br></div><div>Thanks and regards,</div><div>Parul Kudtarkar</div><div><br></div><div>I have attached the configuration file for each step.</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> Your output has no genes. They've all been filtered out. The gene</div></blockquote><div>predictions are left for reference purposes, but there are no gene models</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> in the file. You need to look at the type columns in the GFF3 file --></div></blockquote><div>match/match_part features are evidence and reference data but not</div><div>models.</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> All models will have types gene/mRNA/exon/CDS. For example if you just</div></blockquote><div>want gene models in your file you can use the gff3_merge script with the</div><div>-g option, and it will only print out the gene models.</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> I think you may be misinterpreting what is happening at different steps,</div></blockquote><div>as well as how to read the result files. Could you give me a detailed</div><div>explanation of what you expect to get back together with your control</div><div>files and I can walk you through the configuration, and indicate what to</div><div>expect. Also what was the report like from CEGMA. Could you include the</div><div>report file that shows how complete your genome is and how fragmented it</div><div>is?</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> Thanks,</div><div> Carson</div><div> On 12-12-05 3:03 PM, "Parul Kudtarkar" <<a href="mailto:parulk@caltech.edu">parulk@caltech.edu</a>> wrote:</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>Dear Carson,</div><div>Thanks for a quick response. keep_preds is set to 0</div><div>Though for previous step(ab-intio gene predictions keep_preds was set to</div></blockquote></blockquote><div>1, see Scaffold1_input.gff). I have also attached the output file</div><div>Scaffold1_out.gff.</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>Please advice.</div><div>Thanks and regards,</div><div>Parul Kudtarkar</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> You should always get all predictions, but should only get models</div></blockquote></blockquote></blockquote><div>(match/match_part) with AED scores less than 0.5. You should never get</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> models (gene/mRNA/CDS) with an AED score of 1.00 unless you have</div></blockquote></blockquote></blockquote><div>keep_preds set.</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> Do you have keeps_preds set or gene models with AED values above your</div></blockquote></blockquote></blockquote><div>threshold (not match/match_part features)? If the first one is the</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>case,</div><div> just set it to 0. If the second one in the case, could you send me</div></blockquote></blockquote></blockquote><div>example GFF3?</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> Thanks,</div><div> Carson</div><div> On 12-12-04 7:27 PM, "Parul Kudtarkar" <<a href="mailto:parulk@caltech.edu">parulk@caltech.edu</a>> wrote:</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>Dear Carson,</div><div>Thanks once again, we have limited experimental data with very short</div><div> ESTs.</div><div>CEGMA is useful for us to gauge our gene-model.</div><div>On a different note to re-annotate genome(post evidence based</div><div>prediction(used as training dataset)and abinitio gene-prediction).</div></blockquote></blockquote></blockquote></blockquote><div>Here</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>are the control parameters I am using with AED score set to 0.5,</div><div> however</div><div> I</div><div>get predictions that includes the ones with AED score of 1.00 in</div><div> resulting</div><div>gff3 file. Though I do see the number of genes reduced to 1/3 of</div><div> initial</div><div>gff3 file.</div><div>#-----Genome (Required for De-Novo Annotation)</div><div>genome=Scaffold1.fa #genome sequence file in fasta format</div><div>organism_type=eukaryotic #eukaryotic or prokaryotic. Default is</div><div> eukaryotic</div><div>#-----Re-annotation Using MAKER Derived GFF3</div><div>genome_gff= Scaffold1.gff #re-annotate genome based on this gff3 file</div></blockquote></blockquote></blockquote></blockquote><div>est_pass=1 #use ests in genome_gff: 1 = yes, 0 = no</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>altest_pass=0 #use alternate organism ests in genome_gff: 1 = yes, 0 =</div></blockquote></blockquote></blockquote></blockquote><div>no</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>protein_pass=1 #use proteins in genome_gff: 1 = yes, 0 = no</div><div>rm_pass=0 #use repeats in genome_gff: 1 = yes, 0 = no</div><div>model_pass=1 #use gene models in genome_gff: 1 = yes, 0 = no</div><div>pred_pass=1 #use ab-initio predictions in genome_gff: 1 = yes, 0 = no</div></blockquote></blockquote></blockquote></blockquote><div>other_pass=0 #passthrough everything else in genome_gff: 1 = yes, 0 =</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> no</div><div>#-----MAKER Behavior Options</div><div>AED_threshold=0.5 #Maximum Annotation Edit Distance allowed (bound by</div></blockquote></blockquote></blockquote></blockquote><div>0</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>and 1)</div><div>Thanks and regards,</div><div>Parul Kudtarkar</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> Wow 330,000 is a lot. a large portion of genes are likely to be</div><div>partial</div><div>at</div><div> best. You should seriously consider using mRNAseq to capture those</div></blockquote></blockquote></blockquote></blockquote></blockquote><div>by</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> using maker's est_gff option to pass in results from cufflinks or</div><div>trinity.</div><div> Also I wouldn't even try to annotate contigs less than 10kb in</div></blockquote></blockquote></blockquote></blockquote></blockquote><div>size,</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>just</div><div> have maker skip them by setting the min_contig filter in the</div></blockquote></blockquote></blockquote></blockquote></blockquote><div>maker_opts.ctl file.</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> Thanks,</div><div> Carson</div><div> On 12-11-29 7:31 PM, "Parul Kudtarkar" <<a href="mailto:parulk@caltech.edu">parulk@caltech.edu</a>> wrote:</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>Thanks for the guidance Carson, total contig size is 330,611 with</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>N50</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> of</div><div>39.17kb. I agree we have short ESTs. So this is the possible reason</div><div> when</div><div>filtering based on AED score 0.75 there are no gene models predicted</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>despite the model_gff file has few genes with scores less than 0.75?</div><div>Thanks and regards,</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>Parul Kudtarkar</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> There are certain characteristics that are apparent in this</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>contig.</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>First</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> it seems to be repeat rich with a very low gene density. You also</div><div>have</div></blockquote><div>very short ESTs, and because of the lengths you are probably getting</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>many</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> of them to align spuriously which produces very short gene models</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>that</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>are</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> more than likely false positives or at the very least just a piece</div><div>of</div><div>a</div></blockquote><div>gene. I would turn off est2genome as a predictor for this reason</div><div> unless</div><div>you can get longer EST assemblies (i.e. From mRNAseq). Your</div><div> protein</div><div>alignments also seem to be few and far between. You probably need</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>to</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>add</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> more proteins from a couple of related species, and you might</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>consider</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>using protein2genome rather than est2genome as a predictor if you</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>are</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>still working to generate a training set. Also est2genome produced</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>models</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> almost always have an AED score near 0 so mixing est2genome with</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>the</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>AED_threshold with such limited protein support does create an</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>artificial</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> bias to get back very short and incomplete models.</div><div> How many contigs do you have in total and what is the N50 value</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>for</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>the</div></blockquote><div>assembly? If you have a large number of very short contigs, you will</div><div> get</div><div>very inflated gene counts because you get genes split across contigs</div><div> and</div><div>many contigs tend t be subtle rearrangements of other contigs just</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>assembled in a slightly different way (so you can get bits and</div><div>pieces</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> of</div><div>the same genes just rearranged). This scenario is another</div><div> confounding</div><div>factor if using the est2genome predictor with short ESTs. I would</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>recommend running CEGMA to get an estimate for the genome</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> completeness</div><div>as</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> well as get an estimate of fragmentation as one of the statistics</div></blockquote><div>produced</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> is a percent of genes that are found complete (end to end) vs</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>those</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> that</div></blockquote><div>are partial. CEGMA identifies house keeping genes that tend to be</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>shorter</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> and less intron rich than other genes in the genome, so if CEGMA</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>gives</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> a</div></blockquote><div>high partial percentage and a low complete percentage, then this</div><div> pattern</div><div>can be expected to be even more exaggerated for other genes in the</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>genome.</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> If your genome is highly fragmented or proteins do not align well</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>then</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>there are other strategies. For example, some vertebrate genomes</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>end</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> up</div><div>having extremely fragmented assemblies (on the order of 100,000</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>contigs),</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> and if they are distantly related to other annotated species few</div></blockquote><div>proteins</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> may align to the contigs because the introns in the alignments</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>tend</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> to</div></blockquote><div>be</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> so long and exons so short that it pushes down the significance</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>scores</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>too</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> much. In those cases heavy mRNAseq seems to be the best if not</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>only</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> way</div></blockquote><div>to get enough evidence to stitch gene models together.</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> Thanks,</div><div> Carson</div><div> On 12-11-28 4:40 PM, "Parul Kudtarkar" <<a href="mailto:parulk@caltech.edu">parulk@caltech.edu</a>> wrote:</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>Dear Carson and Daniel,</div><div>Thanks. I ran sample file for filtering genes based on AED score.</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>The</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>input gff3 file was provided to option model_pred(see attached file</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>Scaffold1.gff), the cutoff AED score was set to 0.75. There are at</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> least</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> 5</div><div>genes with AED score less than 0.75. However there were no genes</div><div> predicted</div><div>in the output file(see attached file Scaffold1_out). I have also</div></blockquote></blockquote><div>attached</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>the maker_opts.ctl. Could you please advice on this.</div><div>Thanks and regards,</div><div>Parul Kudtarkar</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> Use the AED_threshold option in the maker_opts.ctl file if you</div><div>just</div><div>want</div><div> to restrict final gene models to close matches directly within</div><div>maker.</div><div>On</div><div> the other hand, if you are trying to build a dataset for</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>training</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> gene</div></blockquote></blockquote></blockquote><div>predictors, use the maker2zff script for generating a filtered</div><div> dataset</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>for</div><div> SNAP training. There are a number of filters available. Just</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>call</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> the</div></blockquote></blockquote></blockquote><div>script once without parameters to see the options.</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> Thanks,</div><div> Carson</div><div> On 12-11-27 5:55 PM, "Daniel Ence" <<a href="mailto:dence@genetics.utah.edu">dence@genetics.utah.edu</a>></div><div>wrote:</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>Hi Parul,</div><div>I think the way you described (with the maker_opts.ctl file) is</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>how</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>you</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>want to proceed. You still need to give the genome too.</div><div>Daniel</div><div>Daniel Ence</div><div>Graduate Student</div><div>Eccles Institute of Human Genetics</div><div>University of Utah</div><div>15 North 2030 East, Room 2100</div><div>Salt Lake City, UT 84112-5330</div><div>________________________________________</div><div>From: <a href="mailto:maker-devel-bounces@yandell-lab.org">maker-devel-bounces@yandell-lab.org</a></div><div>[<a href="mailto:maker-devel-bounces@yandell-lab.org">maker-devel-bounces@yandell-lab.org</a>] on behalf of Parul</div><div> Kudtarkar</div></blockquote></blockquote></blockquote></blockquote><div>[<a href="mailto:parulk@caltech.edu">parulk@caltech.edu</a>]</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>Sent: Tuesday, November 27, 2012 3:41 PM</div><div>To: Parul Kudtarkar</div><div>Cc: <a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a></div><div>Subject: Re: [maker-devel] AED score</div><div>Also, are there any other parameters that are required when</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>filtering</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>based on AED score?</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> Hello Carson,</div><div> Just to confirm, Is there a script that would filter gene</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>models</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>at</div></blockquote></blockquote></blockquote></blockquote></blockquote><div>specific AED score.</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> Alternatively if I were to do this within maker with regards</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>to</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>parameters</div><div> in maker_opts.ctl file I would have to provide my predicted</div><div>genes</div><div>gff3</div><div> file to model_gff and set AED_threshold at desired threshold?</div></blockquote></blockquote></blockquote></blockquote></blockquote><div>Thanks and regards,</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> Parul Kudtarkar</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> AED score with 1 are the ones you don't want. 0 is best and</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>1</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> is</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>worst</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> as</div><div> it is a distance metric. You can use the AED_threshold</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>parameter</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>to</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> require better matching to the evidence by setting it closer</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>to</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>0.</div><div>You</div><div> can</div><div> also try to increase protein homology evidence as some of</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>your</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>calls</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>may</div><div> be split genes due to lack of evidence linking them.</div><div> --Carson</div><div> On 12-11-26 4:35 PM, "Parul Kudtarkar" <<a href="mailto:parulk@caltech.edu">parulk@caltech.edu</a>></div><div>wrote:</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>Dear Maker community,</div><div>For gene-prediction I get training data-set from evidence</div><div> based</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>prediction, I use this data-set to train SNAP as well as Augustus</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>predictions, followed by boot-strapping. I would typically expect</div><div>20-30K</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>genes however I am getting 8 times the expected gene count</div><div> indicating</div><div> too</div><div>many false positives. Is there a way to further refine these</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>predication/script to retain predictions with AED score 1 and if yes</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>how</div><div>to go about this?</div><div>Thanks and regards,</div><div>Parul Kudtarkar</div><div>--</div><div>Scientific Programmer</div><div>Center for Computational Regulatory Genomics</div><div>Beckman Institute,</div><div>California Institute of Technology</div><div><a href="http://www.spbase.org">http://www.spbase.org</a></div><div>_______________________________________________</div><div>maker-devel mailing list</div><div><a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a></div><div><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell</a></div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>-l</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>ab</div><div>.o</div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>rg</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div> --</div><div> Scientific Programmer</div><div> Center for Computational Regulatory Genomics</div><div> Beckman Institute,</div><div> California Institute of Technology</div><div> <a href="http://www.spbase.org">http://www.spbase.org</a></div></blockquote><div>--</div><div>Scientific Programmer</div><div>Center for Computational Regulatory Genomics</div><div>Beckman Institute,</div><div>California Institute of Technology</div><div><a href="http://www.spbase.org">http://www.spbase.org</a></div><div>_______________________________________________</div><div>maker-devel mailing list</div><div><a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a></div><div><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-la">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-la</a></div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>b.</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>or</div><div>g</div></blockquote></blockquote></blockquote></blockquote><div>_______________________________________________</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>maker-devel mailing list</div><div><a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a></div><div><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-la">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-la</a></div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>b.</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>or</div><div>g</div></blockquote><div> _______________________________________________</div><div> maker-devel mailing list</div><div> <a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a></div><div><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab</a></div></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><div>.o</div><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;"><div>rg</div></blockquote><div>--</div><div>Scientific Programmer</div><div>Center for Computational Regulatory Genomics</div><div>Beckman Institute,</div><div>California Institute of Technology</div><div><a href="http://www.spbase.org">http://www.spbase.org</a></div></blockquote></blockquote><div>--</div><div>Scientific Programmer</div><div>Center for Computational Regulatory Genomics</div><div>Beckman Institute,</div><div>California Institute of Technology</div><div><a href="http://www.spbase.org">http://www.spbase.org</a></div></blockquote></blockquote><div>--</div><div>Scientific Programmer</div><div>Center for Computational Regulatory Genomics</div><div>Beckman Institute,</div><div>California Institute of Technology</div><div><a href="http://www.spbase.org">http://www.spbase.org</a></div></blockquote></blockquote><div>--</div><div>Scientific Programmer</div><div>Center for Computational Regulatory Genomics</div><div>Beckman Institute,</div><div>California Institute of Technology</div><div><a href="http://www.spbase.org">http://www.spbase.org</a></div></blockquote></blockquote><div><br></div><div><br></div><div>--</div><div>Scientific Programmer</div><div>Center for Computational Regulatory Genomics</div><div>Beckman Institute,</div><div>California Institute of Technology</div><div><a href="http://www.spbase.org">http://www.spbase.org</a></div><div><br></div><div>--</div><div>Scientific Programmer</div><div>Center for Computational Regulatory Genomics</div><div>Beckman Institute,</div><div>California Institute of Technology</div><div><a href="http://www.spbase.org">http://www.spbase.org</a></div><div><br></div><div><br></div><div><br></div></blockquote></body></html>