<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="">Those are just for name conversion (takes what in the report and rename it to a known DB_xref term). If there is no conversion, the name will stay the same as in the report (unaltered). Different databases have there own db_xref values. I can’t remember where the ones we are using came from (I think it was from GMOD’s Chado database). NCBI also has their own —> <a href="https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/" class="">https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/</a>, Uniprot —> <a href="https://www.uniprot.org/docs/dbxref" class="">https://www.uniprot.org/docs/dbxref</a>, and you can search around for others as well.<div><br class=""></div><div>—Carson</div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On May 24, 2018, at 5:19 PM, Valerie Soza <<a href="mailto:vsoza@uw.edu" class="">vsoza@uw.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi Maker community<br class=""><br class="">I am using the accessory scripts provided with Maker 2.3.19 to do some functional annotations of genes predicted with the Maker pipeline. For integrating information from InterProScan, I want to use the ipr_update_gff script. When I looked at the script, I found the following lines:<br class=""><br class="">my %db_map = (BlastProDom => 'ProDom',<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span> FPrintScan => 'PRINTS',<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span> Gene3D => 'Gene3D',<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span> HMMPanther => 'PANTHER',<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span> HMMPfam => 'Pfam',<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span> HMMPIR => 'PIR',<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span> HMMSmart => 'SMART',<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span> HMMTigr => 'JCVI_TIGRFAMS',<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span> PatternScan => 'Prosite',<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span> ProfileScan => 'Prosite',<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span> );<br class=""><br class="">Does this indicate that these are the only databases that the script will extract information for from an InterProScan report?<br class=""><br class="">I wanted to use all databases currently available from InterProScan 5, InterProScan version 5.28-67.0, see below, but am wondering whether the Maker script will recognize results from all of the following databases?<br class=""><br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>• CDD<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>• COILS<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>• Gene3D<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>• HAMAP<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>• MOBIDB<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>• PANTHER<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>• Pfam<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>• PIRSF<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>• PRINTS<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>• ProDom<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>• PROSITE (Profiles and Patterns)<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>• SFLD<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>• SMART (unlicensed components only by default - this analysis has simplified post-processing that includes an E-value filter, however you should not expect it to give the same match <span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span>output as the fully licensed version of SMART)<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>• SUPERFAMILY<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>• TIGRFAMs<br class=""><br class="">Thanks.<br class=""><br class="">-Valerie<br class=""><br class="">Valerie Soza, Ph.D.<br class="">c/o Hall Lab<br class="">Department of Biology<br class="">University of Washington<br class="">Johnson Hall 202A<br class="">Box 351800<br class="">Seattle, WA 98195-1800<br class="">206-543-6740<br class=""><a href="http://staff.washington.edu/vsoza/" class="">http://staff.washington.edu/vsoza/</a><br class=""><br class=""><br class="">_______________________________________________<br class="">maker-devel mailing list<br class="">maker-devel@box290.bluehost.com<br class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br class=""></div></div></blockquote></div><br class=""></body></html>