Dear All,

I have found a total list of about 3000 transcripts that I am interested in their gene ontology functions. I have the .fasta file of each transcripts. Can anyone advise on how should I go about to extract the GO symbols for each genes?

The pipeline I can think of is input the .fasta file onto GUI-version of Blast2Go and run a remote blast, and then map the GO from Blast2Go. I am already running this right now but it seems quite slow.

Any alternative strategies here? 

regards

Ziyi
<p>Blast2GO is impractially slow in my experience and doesn&#39;t fit well into a Unix pipeline, though that is not the usual target usage. Another approach is <a href="https://github.com/sestaton/HMMER2GO">HMMER2GO</a> if you don&#39;t find a few commands. Here is an example starting with some transcript assemblies called &quot;genes.fasta&quot; and ending with GO terms for each gene/contig.</p>

<pre>
hmmer2go getorf -i genes.fasta -o genes_orfs.faa
hmmer2go run -i genes_orfs.faa -d Pfam-A.hmm
hmmer2go mapterms -i genes_orfs_Pfam-A.tblout -o genes_orfs_Pfam-A_GO.tsv --map</pre>

<p>There is some documenation on the <a href="https://github.com/sestaton/HMMER2GO/wiki/Tutorial">wiki</a> or at the command line and a full <a href="https://github.com/sestaton/HMMER2GO/wiki/Demonstraton">example</a>, as well.</p>
