Parser for BLAST output

This parser is designed for BLAST output with the following options:

program: "blastp" (-p blastp) database: "pdb" (-d pdb) alignment view: "flat master-slave, no identities" (-m 6) GI included in deflines (-I)

The corresponding BLAST command line is something like:

blastcl3 -p blastp -d pdb -e 1e-5 -I -m 6 -o blast.out < fasta_input

You can download network blast client "blastcl3" via anonymous FTP from:

ftp://ncbi.nlm.nih.gov/blast/network/netblast/

fromFile (
        filename,
        blast=Blast,
        db="pdb",
        evalue=1e-5,
        advOpts="",
        )

fromSequence (
        queryName,
        querySeq,
        blast=Blast,
        db="pdb",
        evalue=1e-5,
        advOpts="",
        )