NCBI (especially Kabat) databases

Lawrence P. Casson lpcasson at phoenix.Princeton.EDU
Thu Nov 19 21:21:02 EST 1992


PROBLEM: I would like to retrieve complete mouse T-lymphocyte receptor
variable domain sequences, and avoid having to deal with the small
fragments that constitute many of the GenBank entries.

I'm assuming that the Kabat and Wu database is the best place to start.
In the end, I would like nucleotide sequences that are in GCG format, so
that I can use them with Amplify for the Macintosh.  File transfers by
FTP and TurboGopher are no problem, nor is uncompression or decoding of
various file types.

Is there an easy way to generate individual sequence files from the
dump files in the kabat database at NCBI?  I heard somewhere that there
was a hypercard stack that would do this, although any solution will do.

Is there a better method than downloading kabat database files?  Is it
possible to query a database service in such a way that files with
complete sequences will be returned but not those that contain only
small fragments such as D or J regions?

Thanks for any ideas and suggestions.

Larry Casson
lpcasson at phoenix.princeton.edu



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