<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">fasta_tool with the —trim_maker_utr option.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jun 27, 2021, at 7:55 PM, Sarah Baker <<a href="mailto:vireofeathers@gmail.com" class="">vireofeathers@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><p style="box-sizing:inherit;margin:0px 0px 1em;line-height:1.4285em;color:rgb(51,51,51);font-family:sans-serif;font-size:14px" class="">Hello,</p><p style="box-sizing:inherit;margin:0px 0px 1em;line-height:1.4285em;color:rgb(51,51,51);font-family:sans-serif;font-size:14px" class="">I have annotated several genomes using the Maker2 pipeline with the goal of estimating dN/dS ratios for many genes. </p><p style="box-sizing:inherit;margin:0px 0px 1em;line-height:1.4285em;color:rgb(51,51,51);font-family:sans-serif;font-size:14px" class="">I have been using the <code class="gmail-language-bash" style="box-sizing: inherit; font-family: Consolas, Monaco, "Andale Mono", "Ubuntu Mono", monospace; font-size: 1em; background-color: rgb(245, 242, 240); word-spacing: normal; word-break: normal; line-height: 1.5; padding: 0.1em; border-top-left-radius: 0.3em; border-top-right-radius: 0.3em; border-bottom-right-radius: 0.3em; border-bottom-left-radius: 0.3em;">fasta_merge</code> script to extract the coding sequences, but I just noticed that the nucleotide sequences that it outputs (in *.all.maker.transcripts.fasta) sometimes include the 5' and 3' UTRs and they are not always in the correct reading frame. Is there a way to output CDS sequences in-frame and without UTRs (eg. so that the contents of *.all.maker.transcripts.fasta could be directly translated to the *.all.maker.proteins.fasta output by <span style="font-family: Consolas, Monaco, "Andale Mono", "Ubuntu Mono", monospace; background-color: rgb(245, 242, 240);" class="">fasta_merge</span>)?</p><div style="box-sizing: inherit; margin: 0px; line-height: 1.4285em; color: rgb(51, 51, 51); font-family: sans-serif; font-size: 14px;" class="">Thank you for this great program!</div></div>
_______________________________________________<br class="">maker-devel mailing list<br class=""><a href="mailto:maker-devel@yandell-lab.org" class="">maker-devel@yandell-lab.org</a><br class="">http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org<br class=""></div></blockquote></div><br class=""></div></div></body></html>