Bioperl: Application of bioperl to Genbank flat files

[James Gilbert]

Ian,

Yes, bioperl is the right place to look.  GenBank
parsing is part of the standard Bio::SeqIO system.  
See the documentation.  (There are, however,
problems with the current stable release when
parsing GebBank (but not EMBL).  These are fixed
in the next bug fix release due out this week.)

If you are doing a large scale systematic
analysis, then you may be interested in installing
a local copy of EnsEMBL, since the database has a
better data model for genes than EMBL/GenBank flat
files (not v. difficult).

	James

On Mon, 15 May 2000, Ian Davies wrote:

> Hello there, 
> I am tasked with writing a program that can read and
> parse data from Genbank flat files, as well as ensembl dbs.
> 
> Could someone give me a clue as to whether I am barking
> up the correct  parse tree by looking at Bioperl ?
> - can it read, and also
> represent the level of detail contained
> in the genabank flat files, including feature tables as well
> as sequence info?
> 
> thanks in advance for any help,
> Ian Davies.
> 
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James G.R. Gilbert
The Sanger Centre
Wellcome Trust Genome Campus
Hinxton
Cambridge                        Tel: 01223 494906
CB10 1SA                         Fax: 01223 494919

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