Version 2.0x3 of the FASTA package is available from "ftp.virginia.edu"
in "pub/fasta". This version changes the default alignment method used
for FASTA DNA searches and TFASTA searches back to the older
band-limited Smith-Waterman. Protein searches with FASTA still use a
full Smith-Waterman for alignments, and the full Smith-Waterman is
available for DNA and TFASTA with the "-A" option.
This change was made to improve the performance of FASTA/TFASTA in
searching DNA sequence libraries. Several people had noticed very
slow downs of 5-fold or more with FASTA2.0x. FASTA2.0x is still
slower than earlier versions of FASTA, because it calculates an
"optimized" score for most sequences in the library. This additional
calculation slows the program about 2-fold, but provides a dramatic
increase in sensitivity.
Currently, only the Unix version has been updated.
wrp at virginia.EDU
Dept. of Biochemistry #440
U. of Virginia
Charlottesville, VA 22908