[Bioperl-l] retrieving genomic sequence

Stefan Kirov skirov at utk.edu
Fri Mar 19 10:40:15 EST 2004

You may want to try ensembl API:
let's say you have a file like this:

open (CHR, "<mychr.dat") ||die "File err\n";
while (my $line=<CHR>) {
    chomp $line;
    my ($chr, $start,$end)=split(/,/,$line);
    my $slice = $slice_adaptor->fetch_by_chr_start_end($chr,$start,$end);
    ................do something with it....

To see how to work with ensembl go to http://www.ensembl.org/Docs/ and 
get the tutorial. It is based on Bioperl to some extent, and what you 
want is documented pretty well I believe.
Also see http://www.ensembl.org/Docs/Pdoc/ensembl/.
Hope this helps... amd have fun.

gabriele bucci wrote:

>Hi everibody.
>Does anyone know if I could use BioPerl for retrieving DNA string from  
>multiple specified genomic region?
>I mean, eg: from chromosome 1 starting 1598675 to 1689000, from chr 2 100.... 
>to 101... ecc.
>I'm pretty sure it's possible but as a beginners as I'm I can't find the way 
>trough the various perldocs....
>Thanks to everybody in advance.
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org

Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
1060 Commerce Park, Oak Ridge
TN 37830-8026
tel +865 576 5120
fax +865 241 1965
e-mail: skirov at utk.edu
sao at ornl.gov

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