<html><head><base href="x-msg://96/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>On May 17, 2013, at 3:45 AM, Luciano Abriata wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div ocsi="0" fpstyle="1"><div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0, 0); font-size: 10pt; ">Hello, I am trying to use Maker to annotate genomes from different individuals of a population (D. melanogaster flies).<br><br>My ultimate goal is to get, for each gene, the amino acid sequences of the coded proteins as they are expressed from each genome. My questions are:<br><br>1) How can I match proteins predicted for the same gene in two genomes?<br></div></div></span></blockquote><div><br></div><div>blastp tweaked with parameters to optimize near perfect match</div><br><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div ocsi="0" fpstyle="1"><div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0, 0); font-size: 10pt; "><br>2) What is the meaning of all the data in a line such as the following one (taken from the protein.fasta output)<br><br>maker-2L-augustus-gene-0.19-mRNA-1 protein AED:0.0322873164323667 eAED:0.0322873164323667 QI:2|1|0.66|1|1|1|3|208|541<br><br></div></div></span></blockquote><div><br></div><div>AED = Annotation edit distance describes how closely the prediction matches the evidence. This is a distance measure and thus 0 is a perfect match and 1 is no overlap.</div><div><br></div><div>eAED = Exon adjusted annotation edit distance: This metric is the same as AED with a couple of exceptions. For a protein coding exon to be counted as overlapping protein evidence the reading frame must be the same in the coding exon and the protein evidence. <span class="Apple-style-span" style="font-family: Calibri, sans-serif; font-size: 14px; ">Second, when mRNA Seq data is used as evidence and both ends of an exon are supported with splice site spanning reads, the middle of that exon is counted as supported as well even if coverage drops off in the interior of the exon.. For the most part AED and eAED will always be the same, but eAED tends to work better on many fringe cases.</span></div><div><span class="Apple-style-span" style="font-family: Calibri, sans-serif; font-size: 14px; "><br></span></div><div>QI values are as follows:</div><div><br></div><div><ol class="MailOutline"><li>5' UTR Length</li><li>Fraction of splice sites confirmed by EST alignment.</li><li>Fraction of exons that overlap and EST alignment.</li><li>Fraction of exons that overlap EST or protein alignment.</li><li>Fraction of splice sites confirmed by an ab initio prediction.</li><li>Fraction of exons that overlap an ab intitio prediction.</li><li>Number of exons in the transcript.</li><li>3' UTR length.</li><li>Length of encoded protein.</li></ol></div><div><br></div><br><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div ocsi="0" fpstyle="1"><div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0, 0); font-size: 10pt; ">3) If I include snap and augustus to improve protein predictions, I get several protein.fasta files: augustus_masked.proteins.fasta , snap_masked.proteins.fasta , non_overlapping_ab_initio.proteins.fasta , and proteins.fasta<br><br></div></div></span></blockquote><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div ocsi="0" fpstyle="1"><div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0, 0); font-size: 10pt; ">Which of these files contains the definite set of predicted protein sequences?<br></div></div></span></blockquote><div><br></div><div>The proteins.fasta file is the final set of proteins for all genes that MAKER created annotations for.</div><br><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div ocsi="0" fpstyle="1"><div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0, 0); font-size: 10pt; "><br></div><div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0, 0); font-size: 10pt; "><br></div><div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0, 0); font-size: 10pt; "><br>Thanks in advance!<br><br>Luciano<br></div>_______________________________________________<br>maker-devel mailing list<br><a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a><br><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br></div></span></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><span class="Apple-style-span" style="font-family: Arial; font-size: 12px; "><div>Barry Moore</div><div>Research Scientist</div><div>Dept. of Human Genetics</div><div>University of Utah</div><div>Salt Lake City, UT 84112</div><div>--------------------------------------------</div><div>(801) 585-3543</div><div><br class="khtml-block-placeholder"></div></span></div><div><br></div></span><br class="Apple-interchange-newline">
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