[BiO BB] perl help

Matt McCormick mjmccorm at mtu.edu
Sun Nov 16 16:28:21 EST 2003

Please allow me to elaborate a bit more.  I'm trying to pull a random
100 kb section from the chromosomal sequence(in genbank format,
Accession NC_003070).  The chromosome sequence is 30494425 bp long, and
the positions x and y represent the base i want my sequence to start and
end respectively.  I'm just beginning to use perl, and for me to use
substr function, i would have to find and join all the lines starting at
the ORIGIN.  I m not sure on the best way to do this.  Any help would be
appreciated. Thank you.

On Sat, 2003-11-15 at 19:47, Joe Landman wrote:
> Hi Matt:
> On Sat, 2003-11-15 at 19:33, Matt McCormick wrote:
> > Hi,
> > I am trying to construct a sequence, with start position x and end
> > position y, from A.thaliana chromosome 1.  Does anyone have any code
> > they would be willing to share that would do this? I have the current
> > perl and bioperl modules installed.  Thank you.
>    I might suggest giving a better specification of the problem.  You
> have the chromosome 1 data in some format, and you need to extract a
> particular section from it?  If this is the case, then is there a
> particular reason why the substr function will not work?
> 	my $small = substr $sequence,$x,$y-$x+1 ;
> Joe
> > 
> > -Matt McCormick
> > 
> > 
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