All agains All BLAST

[mhadidi2002]

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,

[GenoMax]

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.

[bioBob]

blastall does this

[mhadidi2002]

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,

[bioBob]

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