You will need bioperl installed.
Check out bioperl (www.bioperl.org) for more info and how to obtain install
bioperl.
use Bio::Tools::Blast;
use Bio::DB::GenBank;
use Bio::SeqIO;
die("usage: blast_fetch blastfile outputfile") if( @ARGV != 2 );
my $db = new Bio::DB::GenBank;
my $blast = Bio::Tools::Blast->new(-file =>@ARGV[0],
-signif => 1e-5,
-parse => 1,
-stats => 1,
-check_all_hits => 1,
);
my $seqio = new Bio::SeqIO(-format=>'Fasta', -file=>">$ARGV[1]");
my ($an,$seq);
foreach my $hit ( $blast->hits) {
(undef,$an) = split(/\|/, $hit->name);
$seq = $db->get_Seq_by_id($an);
if( defined $seq ) {
$seqio->write_seq($seq);
}
}
--
Jason Stajich
jason at nospam-chg.mc.duke.edu
"Neil Saunders" <s3003334 at pop3.unsw.edu.au> wrote in message
news:8nfnin$d8d$1 at mirv.comms.unsw.edu.au...
> I'm currently websurfing for an answer to this problem, but perhaps
someone
> knows a quick answer. Basically, I'm looking for a quick way to download
> sequences obtained from a BLAST search and make a multiple Fasta format
file
> of those hits plus my query sequence. Currently, I do my BLAST search,
then
> click on the accession numbers of the best hits to go to the sequence
> database entry. From there I convert them to Fasta, then copy and paste
> into a new file.
>> A slightly quicker way is to use the 'related sequences' facility from a
> search at NCBI and download all hits as Fasta. But this is still quite
> tedious. What I'd really like is a facility that would parse a BLAST
file,
> extract the top sequences from the database and give them in Fasta format.
> Does anyone know of such a thing?
>> thanks,
>> Neil Saunders
>> --
> School of Microbiology & Immunology,
> University of New South Wales,
> Sydney 2052,
> Australia
>> Ph: +61 2 9385 2093
> Fx: +61 2 9385 1591
> email: neil.saunders at unsw.edu.au>http://www.crosswinds.net/~nfws/index.htm> ArchaeaWeb
>http://www.crosswinds.net/~nfws/archaea/index.htm>>>>>>
