FASTA32 available

William R. Pearson wrp at alpha0.bioch.virginia.edu
Thu Jan 21 11:00:19 EST 1999


A new version of the FASTA3 package of programs - fasta32t01.shar.Z -
is available from ftp://ftp.virginia.edu/pub/fasta.

This version has three major improvements:

(1) DNA sequences are now searched in both orientations by default by
    fasta3 and fastx/y3; as a result, the program is 1/2 as fast, but
    and additional run is not required.  The '-1' option reverts to the
    old single orientation mode.

(2) DNA alignment numbering is now much more sensible.  In particular,
    reverse complement alignments count backwards, and DNA-protein alignments
    use DNA coordinates for the DNA strand, even if a translated protein
    alignment is shown.

(3) There is a new program, fasts3(_t), which searches for unordered
    peptide fragments - reordering the fragments to find the best
    alignment.

Mac and PC versions will be available in a few weeks.

As always, keep those bug reports coming.

Bill Pearson





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