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Old 02-06-2012, 08:00 AM   #1
mhadidi2002
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Default All agains All BLAST

Hello,

I need a tool that can blast proteins sequences in a multifasta file against each other. I mean if there are 10 proteins, I need to blast each one of the ten with the other 9, and reports significant hits.
I used before avaBLAST, but now I can't find the download files.

Thanks,
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Old 02-06-2012, 09:21 AM   #2
GenoMax
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Blat can do this easily: http://users.soe.ucsc.edu/~kent/src/
You will need to decide on a output format that suits your purpose and perhaps do some scripting to fish out results you need.
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Old 02-07-2012, 03:25 AM   #3
bioBob
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blastall does this
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Old 02-07-2012, 07:10 AM   #4
mhadidi2002
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Quote:
Originally Posted by bioBob View Post
blastall does this
Hello

Thanks for the reply..
I typed the following command:
makeblastdb -in good_proteins.fasta -dbtype prot -out my_prot_blast_db

But I can't find the output. can u please how can I retrieve the output?

Thanks,
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Old 02-07-2012, 07:26 AM   #5
bioBob
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all you have accomplished with that command is to format the db, now you need to actually do the blastall, here is what I use for the older blastall

formatdb -i good_proteins.fasta -p T
blastall -i good_proteins.fasta -d good_proteins.fasta -o results -m 8
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