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 |
>|--------------------------------------------------------------------|
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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 |
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