FASTA 1.6 deja vu again

Bill Pearson wrp at cyclops.micr.Virginia.EDU
Fri Jan 10 11:16:51 EST 1992

	It is with some embarrasment that I announce yet another revison
of the FASTA 1.6 version - 1.6b2.  Now available on uvaarpa.virginia.edu is:

	fasta16b2.shar and fasta16b2.shar.Z

These versions fix a trivial problem with numbers in alignments (which
arose because fasta now allows negative offsets in alignments; this is
useful for aligning upstream 5'-flanking regions) and a somewhat more
serious problem which occured when one was optimizing every sequence
in a library.

	The optimization problem appeared because for the first time,
doing a search with ktup=1 and optimizing every sequence in the
library takes only about twice as long as doing the search with ktup=1
and optimizing only a few sequences.  (In the past, it usually took
about 5 times longer to do a fully optimized search).  As a result,
for protein sequences, it is very practical to search an entire
database with ktup=1, optimizing every sequence (This takes about 15
min on a 25 Mhz Sun 4 with a 200 residue query sequence against PIR
release 30 - 10,000,000 residues in 34,000 entries).  When I started
optimizing large libraries, I uncovered some bugs in how the best
scores were saved with optimization.

	A FASTA search with ktup=1, optimizing all sequences, compares
very favorably with a rigorous Smith-Waterman search (ssearch, see
Pearson (1991) Genomics, 11:635) and takes about 1/7 as long with this

	With luck, fasta16b2 will be stable for more than a few days.

Bill Pearson

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