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

[avilella]

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.