[Bioperl-l] Is bio-perl right?

John S. J. Anderson janderso@ncbi.nlm.nih.gov
28 Sep 2000 22:11:47 -0400

Greetings --

I'm trying to decide if bio-perl provides the tools I need to do
something, or if I'm better off rolling my own custom solution.

Basically, I want to retrieve a large number (hundreds) of sequence
files from Genbank (via Entrez, so there are a number of potential
formats) and then parse each file according to the header
information. I need to split the sequence in each file into coding and
non-coding, and I would like to map each segment back onto a genome
(probably by tracking location relative to ORF starts and stops).

I know there's been some traffic on the list recently about the
difficulty of sufficiently generalizing the GenBank format via a
bio-perl parser, but I haven't played around with the code at all. (To
cross with another thread, the documentation (and lack of time) has
been the biggest barrier to my picking up bio-perl.)

So, is bio-perl the Right Thing for this job, or should I look into
developing my own stuff?

Thanks for any advice,

John S J Anderson                                           NCBI,NLM,NIH
IRTA Fellow                                              Bldg 38A, B2N14  
janderso@ncbi.nlm.nih.gov                                   301.594.6087