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How Do I Tell Blast To Search Multiple Database Using Bio::tools::run::standaloneblast?

Answer»

PUT the names of the databases in a variable. LIKE so:

my $dbs = '"/dba/BMC.fsa /dba/ALC.fsa /dba/HCC.fsa"';
my @params = ( d => "$dbs",
program => "BLASTN",
_READMETHOD => "Blast",
outfile => "$dir/est.bls" );

my $FACTORY =
Bio::Tools::RUN::StandAloneBlast->new(@params);
my $seqio = Bio::SeqIO->new(-FILE=>'t/amino.fa',-format => 'Fasta' );
my $seqobj = $seqio->next_seq();
$factory->blastall($seqobj);

Put the names of the databases in a variable. like so:

my $dbs = '"/dba/BMC.fsa /dba/ALC.fsa /dba/HCC.fsa"';
my @params = ( d => "$dbs",
program => "BLASTN",
_READMETHOD => "Blast",
outfile => "$dir/est.bls" );

my $factory =
Bio::Tools::Run::StandAloneBlast->new(@params);
my $seqio = Bio::SeqIO->new(-file=>'t/amino.fa',-format => 'Fasta' );
my $seqobj = $seqio->next_seq();
$factory->blastall($seqobj);


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