This package exports the ExecBlast method, which can be used to perform a BLAST from a FASTA file against one or more genomes.
The tool table is a hash that provides useful information about each blast tool. The hash maps each tool name to a hash reference. The various fields in the hashes are as follows.
Type of database against which the tool runs: prot for a protein database and
dna for a DNA database.
my @sims = ExecBlast($fig, $seqFile, \@genomes, $tool, $options);
Call BLAST to compute the similarities for a sequence.
A FIG-like object for accessing the data store.
Name of a file containing the sequence to blast in FASTA format.
A list of the IDs for the target genomes of the blast.
Name of the blast tool to use.
Options to pass to the blast tool, formatted for the command line.
Returns a list of similarity objects, each representing a segment similar to the incoming sequence.
CallBlast::VerifyDB($db, $type);
Verify that the specified FASTA file has BLAST databases. If the databases do not exist, they will be created. If they are older than the FASTA file, they will be regenerated.
Name of the FASTA file.
Type of database desired: prot for protein and dna for DNA.