[Bioperl-l] Parsing Genbank

Brandi Cantarel bcantarel at som.umaryland.edu
Wed Dec 2 13:36:27 EST 2009

Hi all,
I am not sure if this is normal, but when I use SEQIO to parse genbank files, it changes the coordinates of things on the minus strand.

For example, I have a sequence that has a CDS on the minus strand at it is from 911 to 974.  The sequence is 974 nt.

x $cds->start
x $cds->end

How can I get the original coordinates?  Is there a command for that or will I have to just do the math?

Feature or Bug?

Brandi Cantarel, PhD
Bioinformatics Analyst
Institute for Genome Sciences
School of Medicine
University of Maryland, Baltimore

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