Batch BLASTP

[mith]

This might seem silly but I'm thinking of running a genome(lactic acid bacteria) thru a gene predictor program and throwing the amino acid sequences into blastp.

There's a batch version online but I don't have the password for the site .

Alternatives?

[G-Do]

You could run the sequence through FGENESB:

http://www.softberry.com

To get to FGENESB, mouse over "OPERON & GENE FINDING IN BACTERIA" in the left-hand navigation bar and select FGENESB. This tool lets you annotate genes on an input genome using a Markov chain trained on some similar organism. In the output, it gives you an index of where each predicted gene appears, then a FASTA-formatted list of each predicted peptide. You could run the predictor, then copy the FASTA part of the results into the batch BLAST server at SWBIC and run blastp against the nr protein database:

http://darwin.nmsu.edu/cgi-bin/nmsu/batch_blast.cgi

Of course, it's not as nice as having a server where you just input the genome and get orthologs, but it's still a lot less work than trying to BLAST each predicted peptide manually, or writing your own script.

Hope that helps!

[mith]

Thanks, I found another website that does batch blasting without need for passwords