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protein sequence

Richard Durbin rd at mrc-lmb.cam.ac.uk
Fri Dec 30 06:07:23 EST 1994


The public release version 2 of ACEDB will not accept protein sequence.
He have, however, added that feature some time ago, and the more recent
version 3 releases should accept protein sequence in class Peptide, not
AA, in the same type of format as DNA, e.g.

Peptide HBA_HUMAN
VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA
VHASLDKFLASVSTVLTSKYR

The new version 4 (coming soon) will contain this code to parse and dump
amino acid sequences, and there will also be a protein display package like
the DNA display -- probably very basic in the first release.

Note that if protein sequences are present, they are used by the blixem
multiple alignment viewer, in place of external fetched sequences.  This
is simpler to maintain, and substantially faster.

Richard




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