GenPept, do we need it?

Mark A. Gunnell GUNNELL at FCRFV1.NCIFCRF.GOV
Sun Feb 14 23:50:58 EST 1993


Stephen -

> The announcement by Mark Gunnell of the Genpept rel.75 reminds me of a
> question I have always had about Genpept. If the translation of the ORF of a
> sequence in Genbank is within the description why can't the search programs
> use this information to do protein searches instead of having another
> database with all of its redundant data (i.e. Genpept)? Does Genpept have
> more ORF translations than exist in the nucleic acid database's description
> section of each record? 
  
No, GenPept is derived _entirely_ from the the "/translation=" features
in Genbank.  As an administrator of sequence data, I know I am always looking
for a way to conserve disk space, so I am hoping the next generation of
searching software will be able to use the raw data of Genbank more 
intelligently.  Until then, since I'm creating GenPept anyway, I thought 
I'd make it available to anyone else who needs it.

> Would it be a good idea to update the search programs and phase out Genpept?

Absolutely,  I'm anticipating the day that GenPept is no longer useful as a
separate database.

>|--------------------------------------------------------------------|
>| Stephen Baird                         baird at labsun1.med.uottawa.ca | 
>| Molecular Genetics                       tel: 613-738-3925         |
>| Children's Hospital of Eastern Ontario   fax: 613-738-4833         |
>| 415 Smyth Rd.                                                      |
>| Ottawa, Ontario                                                    |
>| Canada                                                             |
>|--------------------------------------------------------------------|
-------------------------------------------------------------------------------
Mark A. Gunnell                   | Internet: gunnell at ncifcrf.gov
Sci. Applications Analyst         | Bitnet:   gunnell%ncifcrf.gov at cunyvm.bitnet
Biomedical Supercomputer Center   | Phone:   (301) 846-5779
PRI/DynCorp                       |
NCI-FCRDC                         |
PO Box B, Bldg 430                |
Frederick, MD 21702-1201  USA     |
-------------------------------------------------------------------------------




More information about the Bio-soft mailing list