<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><div><div>1. yes. It should take NCBI BLAST+ results.</div><div>2. It has to be UniProt/Swissprot or you can modify the comments of another database to look like UniProt/Swissport </div><div>3. ipr_update_gff, can also take BLAST2GO results as an undocumented feature (or at least it could last time I tested it - which was quite a long time ago).</div><div><br></div><div>Thanks,</div><div>Carson</div></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Guohong Cai <<a href="mailto:caigh02@gmail.com">caigh02@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Sunday, February 9, 2014 at 8:26 PM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Fwd: Functional annotation of MAKER gene models<br></div><div><br></div><div dir="ltr">I sent the following message to Carson but forgot to send to the maker-devel list<br><div><div class="gmail_quote"><br><div dir="ltr"><div><div><div><div><div><div><div>Hi Carson,<br><br></div><div>Again need your help!<br><br></div>With your guidance, I have the gene models for my genomes. Now I am trying to assign functions to the gene models. I noticed that I can use maker_functional_gff/fasta or interproScan. I dig out some old messages in maker-devel google group, but still have a few questions:<br><br></div>1. Will maker_functional_gff/fasta take NCBI blastp results, or only wu-blast results? I do not have wu-blast.<br><br></div>2. Do I have to use Uniprot/Swiss_prot database or I can use something else? For example, may I add a few high-quality genome annotations of related species to the swiss_prot database? Or may I use Uniref90 or nr database instead of swiss_prot?<br><br></div>3. Do you have a script to integrate blast2go results to the maker gff/fasta? <br><br></div>Thanks.<br><br></div>Guohong<br><br></div>Rutgers University <br></div></div><br></div></div>
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