[Bioperl-l] Downloading a sequence in genbank format - related problem

Diogo Tschoeke diogoat at gmail.com
Thu May 17 18:14:14 UTC 2007


Hi Barry thank's for all your help,

I choose download the Invertebrates division of NCBI to machine...
but the I don't have thus script to get the sequences of the local file and
I know how to write...
i tried choose change in the script
the -db => 'nucleotide' for -db => 'local-gbdi.gb'
like I wrote below

my $query = Bio::DB::Query::GenBank->new
                                (-query   =>'Leishmania major',
                                -db     => '>local-gbdi.gb );
my $gb = new Bio::DB::GenBank;
my $seqio = $gb->get_Stream_by_query($query);

but didn't work because de Bio:DB::Query::GenBank is a perl module wich
conect at Ncbi to do my query and my Database is now local.

 I need the genomes of Trypanosoma cruzi, Trypanosoma brucei, Leishmania
major, Entamoeba and Plasmodium falciparum in the genbank format file.
Any Sugestion? Somebody have this script?
Help!
And thank's for the help!

Diogo Tschoeke
Laboratory of Molecular Biology of Trypanosomatides
Fundação Osvaldo Cruz - Fiocruz RJ, Brazil
http://biowebdb.org




More information about the Bioperl-l mailing list