NCBI (especially Kabat) databases

cherry at OPAL.MGH.HARVARD.EDU cherry at OPAL.MGH.HARVARD.EDU
Sat Nov 21 10:27:06 EST 1992


>In article <1992Nov20.022102.12238 at Princeton.EDU>, lpcasson at phoenix.Princeton.EDU (Lawrence P. Casson) writes:
>>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.

I do not know of anyone that has indexed the Kabat databases and
provides a mechanism to retrieve individual sequences.

I have converted the Kabat amino acid database into GenPept format so
that the GCG utilities can be used. I used the Kabat 5.0 (beta) amino
acid database.  It is available via anonymous ftp from
amber.mgh.harvard.edu as follows:

cd genbank
get kabat.genpept

Once on your system you can use: GENBANKTOGCG/GENPEPT to convert this
text file into a GCG formated database. After then running SEQCAT you
can use STRINGS and FETCH to retrieve the specific sequences you want.

Mike Cherry



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