[Bioperl-l] Mapping between aligment position and reference (1st) sequence position for MAF files

Jason Stajich jason at cgt.duhs.duke.edu
Wed Apr 21 13:22:41 EDT 2004

If I understand your question correctly...

I've added a method to Bio::Coordinate::Utils for getting the alignment
position (column) for a specific position in the reference sequence.  It
is called from_seq_to_alignmentpos().

If you want to get the reverse - a reference position from the alignment
you should just be able to do:
my $seq = $aln->get_seq_by_pos(1);
my $ref_loc = $se->location_from_column($column);

# see what that position is:
print $ref_loc->to_FTstring(),"\n";


On Wed, 21 Apr 2004, avilella wrote:

> Hi,
> I was wondering which is the best way to get a mapping between the
> alignment position of a MAF file and the reference sequence position, in
> that case for the first individual in the file.
> I would like to be able to associate the result of an analysis for a
> position in a MAF alignment to the reference sequence.
> If not being done before, which is the best place to implement that?
> Thanks,
>     Albert.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

Jason Stajich
Duke University
jason at cgt.mc.duke.edu

More information about the Bioperl-l mailing list