[Bioperl-l] Help on a basic EST-genomic alignment script

[Edward Chuong]

Hey,

I just did this on a ~180mb file (the gbff file from
ftp://ftp.ncbi.nih.gov/refseq/M_musculus/mRNA_Prot/)

use Bio::Index::GenBank;
...


    274 
    275         my $mus_gbff = "$BLAST_DBs/musRNA/mouse.rna.gbff";
    276 
    277         my $inx = Bio::Index::GenBank->new ('-filename' =>
$mus_gbff . ".idx",
    278                                             '-write_flag' => 'WRITE');
    279         $inx->make_index ($mus_gbff);
    280 
    281         my $hit_full_seq = $inx->get_Seq_by_acc ($accession);
    282 
The program took an incredibly long time and slowed the computer down
to a crawl, so I went home after 30 minutes (so I can't really check
if it works) but last I checked the resulting idx was approaching 8gb.
Does this sound right..? I've googled and found little.

Thanks,

Ed
-- 
Edward Chuong
http://iacs5.ucsd.edu/~echuong