BLAST comparison between two sets of sequences

Peppe · 10-03-2014, 08:03 AM

Hello everyone,
I have a set of sequences generated with Trinity and I want to compare them with S. cerevisiae. I have downloaded the S. cerevisiae protein set from the SGD. Since S. cerevisiae is a reference organism, I need to name my transcripts using S. cerevisiae nomenclature.
For the comparison I used BLASTx. Although the BLASTx itself is quite easy to do using the Windows version of BLAST 2.2.29+, I run into the problem that I cannot get S. cerevisiae gene names.

As an example, one protein is indicated as
>YAL001C TFC3 SGDID:S000000001, Chr I from 151006-147594,151166-151097, Genome Release 64-1-1, reverse complement, Verified ORF, "Largest of six subunits of the RNA polymerase III transcription initiation factor complex (TFIIIC); part of the TauB domain of TFIIIC that binds DNA at the BoxB promoter sites of tRNA and similar genes; cooperates with Tfc6p in DNA binding"

I run BLASTx using several flags (eg -outfmt 6 or -outfmt 7 -qseqid -sseqid -stitle), but the only thing that I get is the systematic name (i.e. YAL001C) but not the gene name and the description (i.e. TFC3 etc.).

Have anybody run into the same problem? Do you guys have any advice? Doing manually the blast one by one of ~1000 sequences is going to drive me nuts!
Thanks a lot

GenoMax · 10-03-2014, 08:25 AM

Cross-posted here: http://seqanswers.com/forums/showthread.php?t=47167

Please use that thread for solutions.

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10-03-2014, 08:03 AM	#1
Peppe Member Location: USA Join Date: Nov 2012 Posts: 11	BLAST comparison between two sets of sequences Hello everyone, I have a set of sequences generated with Trinity and I want to compare them with S. cerevisiae. I have downloaded the S. cerevisiae protein set from the SGD. Since S. cerevisiae is a reference organism, I need to name my transcripts using S. cerevisiae nomenclature. For the comparison I used BLASTx. Although the BLASTx itself is quite easy to do using the Windows version of BLAST 2.2.29+, I run into the problem that I cannot get S. cerevisiae gene names. As an example, one protein is indicated as >YAL001C TFC3 SGDID:S000000001, Chr I from 151006-147594,151166-151097, Genome Release 64-1-1, reverse complement, Verified ORF, "Largest of six subunits of the RNA polymerase III transcription initiation factor complex (TFIIIC); part of the TauB domain of TFIIIC that binds DNA at the BoxB promoter sites of tRNA and similar genes; cooperates with Tfc6p in DNA binding" I run BLASTx using several flags (eg -outfmt 6 or -outfmt 7 -qseqid -sseqid -stitle), but the only thing that I get is the systematic name (i.e. YAL001C) but not the gene name and the description (i.e. TFC3 etc.). Have anybody run into the same problem? Do you guys have any advice? Doing manually the blast one by one of ~1000 sequences is going to drive me nuts! Thanks a lot Last edited by Peppe; 10-03-2014 at 08:08 AM.

10-03-2014, 08:25 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,091	Cross-posted here: http://seqanswers.com/forums/showthread.php?t=47167 Please use that thread for solutions.