4 replies to this topic

[cardosopedro]

Hi.

Can someone tell me if it is possible to do a simultaneous BLAST for several proteins?

I'm trying to analyse by BLAST the similarities between cell death proteins of the filamentous fungus Neurospora crassa and Homo sapiens. For instance, I have the list of H. sapiens' "programmed cell death-associated molecules" from geneontology.org. I want to BLAST this molecules against a N. crassa database. Will I have to do it one-by-one?

Thanks!

[pcrman]

Some databases allow you to do that. You just need to organize your sequences in FASTA format and put them in one file. Then upload or paste the content of the file to BLAST program.

[cardosopedro]

Ok, thanks.

But still, let's say that I'm trying to BLAST hundreds of molecules. Is it possible to BLAST them all at once? Is it possible to get a .txt with FASTA sequences of them all at once?

[HomeBrew]

You should look at NetBLAST (see here), aka "blastcl3".  It is a command-line utility that will allow you to BLAST many sequences at once, retaining the results in a single file.

To do things like this more rapidly (e.g. on a genomic scale), I have also used custom local databases and Perl scripts to perform the BLAST and parse the output files, using the command line utility blastall (see here).

[cardosopedro]

HomeBrew, on Jun 3 2009, 05:34 PM, said:

You should look at NetBLAST (see here), aka "blastcl3".  It is a command-line utility that will allow you to BLAST many sequences at once, retaining the results in a single file.

To do things like this more rapidly (e.g. on a genomic scale), I have also used custom local databases and Perl scripts to perform the BLAST and parse the output files, using the command line utility blastall (see here).

Thanks.