JPRED-2 Add sources of all binaries (except alscript) to Git

[jpred.git] / sources / pairwise / README

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+Wed Dec  5 14:33:35 GMT 2001
+JDB
+
+This program takes a FASTA file, and produces a OC input file as
+output. The FASTA file should be an alignment. The code finds the begining
+and end of the sequence in each alignment, the number of residues for
+in each sequence, and then does an all against all pairwise identity
+calculation. This is the number of identical residues divided by the
+number of residues in the longest sequence, shared gaps are ignored. A
+percentage is returned.
+
+BUGS
+Very little error checking is done on the filling of the structures with
+FASTA data.
+It seems quite slow to do the pairwise comparisons.