<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="">The domain info goes in the the database cross reference field according to GFF3 format. We put any functional info in the Note field as it essentially works as a description according the GFF3 best practices. You can also use iprscan2gff3 to create gff3 features corresponding to the position of domains that can be loaded into a browser. If you want domain or go info inside of the Note field of the GFF3 or in the fasta header, you would need to make your own scripts for that. Note that browsers like Browse can be configured to link out to appropriate websites for values in the Dbxref attribute.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Nov 1, 2020, at 5:45 PM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" class="">eennadi@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class="">Hi Carson,<div class="">Please I will like to know how to combine the gff results obtained using <span style="font-family:Courier;font-size:11px" class="">ipr_update_gff and the gff obtained using </span><span style="font-family: Menlo; font-size: 11px;" class="">maker_functional_gff? </span></div><div class=""><span style="font-family: Menlo; font-size: 11px;" class="">For example the </span><span style="font-family: -webkit-standard; font-size: inherit;" class="">ipr_update_gff adds the following to the gff </span></div><div class=""><span style="font-family: Menlo; font-size: 11px;" class=""><br class=""></span></div><div class=""><span style="font-family: Menlo; font-size: 11px;" class="">scaffold_252</span><span style="font-family: Menlo; font-size: 11px;" class=""> </span><span style="font-family: Menlo; font-size: 11px;" class="">maker </span><span style="font-family: Menlo; font-size: 11px;" class=""> </span><span style="font-family: Menlo; font-size: 11px;" class="">gene</span><span style="font-family: Menlo; font-size: 11px;" class=""> </span><span style="font-family: Menlo; font-size: 11px;" class="">22873 </span><span style="font-family: Menlo; font-size: 11px;" class=""> </span><span style="font-family: Menlo; font-size: 11px;" class="">47327 </span><span style="font-family: Menlo; font-size: 11px;" class=""> </span><span style="font-family: Menlo; font-size: 11px;" class="">. </span><span style="font-family: Menlo; font-size: 11px;" class=""> </span><span style="font-family: Menlo; font-size: 11px;" class="">- </span><span style="font-family: Menlo; font-size: 11px;" class=""> </span><span style="font-family: Menlo; font-size: 11px;" class="">. </span><span style="font-family: Menlo; font-size: 11px;" class=""> </span><span style="font-family: Menlo; font-size: 11px;" class="">ID=CR513_001491;Name=CR513_001491;Alias=augustus_masked-scaffold_252-processed-gene-0.0;Dbxref=InterPro:IPR000719,Pfam:PF00069;Ontology_term=GO:0004672,GO:0005524,GO:0006468; </span><span style="font-family: Menlo; font-size: 11px;" class=""> </span><span style="font-family: Menlo; font-size: 11px;" class="">ID=CR513scaffold_252</span><span style="font-family: Menlo; font-size: 11px;" class=""> </span><span style="font-family: Menlo; font-size: 11px;" class="">maker </span><span style="font-family: Menlo; font-size: 11px;" class=""> </span><span style="font-family: Menlo; font-size: 11px;" class="">mRNA</span><span style="font-family: Menlo; font-size: 11px;" class=""> </span><span style="font-family: Menlo; font-size: 11px;" class="">22873 </span><span style="font-family: Menlo; font-size: 11px;" class=""> </span><span style="font-family: Menlo; font-size: 11px;" class="">47327 </span><span style="font-family: Menlo; font-size: 11px;" class=""> </span><span style="font-family: Menlo; font-size: 11px;" class="">. </span><span style="font-family: Menlo; font-size: 11px;" class=""> </span><span style="font-family: Menlo; font-size: 11px;" class="">- </span><span style="font-family: Menlo; font-size: 11px;" class=""> </span><span style="font-family: Menlo; font-size: 11px;" class="">. </span><span style="font-family: Menlo; font-size: 11px;" class=""> </span><span style="font-family: Menlo; font-size: 11px;" class="">ID=CR513_001491-RA;Parent=CR513_001491;Name=CR513_001491-RA;Alias=augustus_masked-scaffold_252-processed-gene-0.0-mRNA-1;Dbxref=InterPro:IPR000719,Pfam:PF00069;Ontology_term=GO:0004672,GO:0005524,GO:0006468;_AED=0.50;_QI=0|0.08|0.04|0.16|1|1|25|0|927;_eAED=0.50;_merge_warning=1;</span><span style="font-family: Menlo; font-size: 11px;" class=""> </span></div><div class=""><font face="Menlo" class=""><span style="font-size:11px" class=""><br class=""></span></font></div><div class=""><font face="Menlo" class=""><span style="font-size:11px" class="">While </span></font></div><div class=""><span style="font-family: -webkit-standard; font-size: inherit;" class="">maker_functional_gff</span></div><div class=""><span style="" class=""></span><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">scaffold_252 maker gene 22873 47327 . - . ID=CR513_001491;Name=CR513_001491;Alias=augustus_masked-scaffold_252-processed-gene-0.0;Note=Similar to IREH1: Putative serine/threonine protein kinase IREH1 (Fragment) (Mucuna pruriens OX%3D157652);scaffold_252 maker mRNA 22873 47327 . - . ID=CR513_001491-RA;Parent=CR513_001491;Name=CR513_001491-RA;Alias=augustus_masked-scaffold_252-processed-gene-0.0-mRNA-1;_AED=0.50;_QI=0|0.08|0.04|0.16|1|1|25|0|927;_eAED=0.50;_merge_warning=1;Note=Similar to IREH1: Putative serine/threonine protein kinase IREH1 (Fragment) (Mucuna pruriens OX%3D157652); (Fragment) (Mucuna pruriens OX%3D157652);</span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class="">Is there a way of making maker reflect the GO and pfam alongside the functional names?</div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><br class=""></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><br class=""></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class="">Also, how can this be reflected in the corresponding protein and transcript fastas?</div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><br class=""></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class="">Thanks for your support.</div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><br class=""></div><div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><br class=""></div><div class=""><div dir="ltr" class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class="">Nnaemeka Emmanuel Nnadi,Ph.D<div class="">Department of Microbiology,</div><div class="">Faculty of Natural and Applied Science,</div><div class="">Plateau State University, Bokkos, Plateau State, Nigeria.</div><div class="">+2348068124819</div><div class="">Publications: </div><div class=""> <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank" class="">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</a></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
</div></blockquote></div><br class=""></div></body></html>