I need to extract given pieces of sequence from a set of EMBL/GenBank
flat file entries (as retrieved from NCBI's email server), using ranges
defined in the features table. For example, I'd like to be able to
extract, from a set of entries, the DNA sequence for each exon, or
again for every complete CDS feature (all exons assembled).
Surely not everyone does this manually?
What software exists that can actually parse the (eminently parsible)
joint features table format? Please post reviews of programs you have
used, or mail me directly and I will summarize.
-- Will Fischer