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Simultaneous BLAST for several proteins


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4 replies to this topic

#1 cardosopedro

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Posted 02 June 2009 - 07:53 AM

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!

#2 pcrman

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Posted 02 June 2009 - 09:16 AM

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.

#3 cardosopedro

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Posted 03 June 2009 - 03:36 AM

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?

#4 HomeBrew

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Posted 03 June 2009 - 08:34 AM

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).

#5 cardosopedro

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Posted 03 June 2009 - 08:43 AM

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.




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