If your or other readers language tastes are diverse enough to include
java, the new Readseq package makes programming sequence feature
extraction and manipulation relatively easy.
Readseq creates feature objects (lists & hashes...) when reading
GenBank and EMBL format data. You can use these to extract, remove or
manipulate sequence subsets by feature name or by seq. range.
See for a short example feature extraction program see
I've updated the readseq.jar archive to version 2.0.5
to provide easier interfaces for programming of feature table uses.
Source code to the package is available, but you may not need it for
writing programs that use it. The readseq.jar plus some examples and
the api docs
may be enough to get you started.
-- gilbertd at bio.indiana.edu