Kabat database usage with Wisconson Package(GCG)

Peter Rice pmr at sanger.ac.uk
Wed Oct 23 03:36:22 EST 1996


In article <hergtp-1610961040580001 at aipgw226.worceste.basf-corp.com> hergtp at basf-corp.com (Paul L. Hergt) writes:
>   Has anyone built a tool to convert the the current Kabat databases to a
>   format the Wisconson Package (GCG) can use.  I know of kabattogcg that is
>   part of the
>   EGCG package from Dr. Rice &al in the UK.  The routine was written by
>   Rodrigo Lopez.

Well, assuming you have GCG already you can install EGCG for free.

Also, GCG format is really very simple - you just need a script (or
a short program) to split the sequence and reference information into
two files, create a header file, and use the GCG DBINDEX program to build
the rest. That is all KABATTOGCG and similar programs really do.

But aside from that, with Kabat there is also an issue of what format
you really want to use the databases in: just a simple sequence database
or as a set of alignments. Both can, in theory, be used with GCG.
--
------------------------------------------------------------------------
Peter Rice                           | Informatics Division,
E-mail: pmr at sanger.ac.uk             | The Sanger Centre,
Tel: (44) 1223 494967                | Wellcome Trust Genome Campus,
Fax: (44) 1223 494919                | Hinxton, Cambridge, CB10 1SA,
URL: http://www.sanger.ac.uk/~pmr/   | England




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