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<div><span></span>Dear sir:</div><div> I¡®ve been using maker to do my genome annotation. However, I still have something I can't understand:</div><div><br></div><div> 1. After assembly, I have many contigs. Firstly, I set est2genome=1 and protein2genome=1 , with my proteins, ESTs and RNA-seq.. <b>Which way below is correct?</b></div><div> 1.1 Each contig has its own gff. I just use its own maker_gff file to get a pyu.hmm(be used in snap practice), and then, train the single contig.</div><div> 1.2 I merge all the maker_gff to produce a pyu.hmm(for snap) , and then, use this pyu.hmm to train all the contigs.</div><div> </div><div> 2. The aim of my project is to find new protein, so I need to guarantee the rigor of my annotation.</div><div> <b>I made a plan that the predicted protein should be successfully aligned to the Uniprot(reviewed protein, total number is about 30K) with 100% identity and coverage.</b></div><div> However, if I choose method 1.2 as above:</div><div> After the first step (est2genome=1 and protein2genome=1), about 1600 proteins can be 100% aligned to the Uniprot. After 2 rounds training(est2genome=0 and protein2genome=0), less proteins can be 100% aligned.</div><div> <b>Is my test method reasonable? Why the final results can't get more well aligned proteins?</b></div><div><b> </b><b style="font-size: 10.5pt; line-height: 1.5; background-color: window;">After training and fasta_merge, the results can be </b><span style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;">index_all.log.all.maker.proteins.fasta, </span><span style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;">index_all.log.all.maker.snap_masked.proteins.fasta, </span><span style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;">index_all.log.all.maker.non_overlapping_ab_initio.proteins.fasta, which is the final results?</span></div><div><span style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;"><br></span></div><div><span style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;"> </span></div><div><span style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;"> I'm looking forward to hearing from you. Thanks!</span></div><div>Yours sincerely!</div><div><br></div><div> </div>
<div>Chao Chao</div><hr style="width: 210px; height: 1px;" color="#b5c4df" size="1" align="left">
<div><span><div style="MARGIN: 10px; FONT-FAMILY: verdana; FONT-SIZE: 10pt"><div>dcg@cau.edu.cn</div></div></span></div>
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