[Biojava-l] Question about cutting a sequence

Stein Aerts stein.aerts@esat.kuleuven.ac.be
Fri, 20 Sep 2002 15:18:07 +0200

I've had these questions since I started using Biojava a year ago, and I
still can't get it right:

1. How can I take a certain part of an annotated sequence (let's say from bp
500 to 750), make a new sequence from this part, while retaining all
annotations of the piece, in new coordinates? So a feature on the original
sequence from 600 to 610 has to be the same feature with its annotation, on
the subsequence from 100-110.

2. If I'm using DNA sequences, and if I need the strand of my features, then
I get Exceptions when a certain feature is not stranded. So in the first
case I need a StrandedFeature, in the second a Feature, but that puzzles me.

Any ideas or examples?

Thank you!
Stein Aerts.