Release 1.6b of the FASTA package of sequence comparison
programs is now available for anonymous ftp from uvaarpa.virginia.EDU.
Changes from release 1.6a2 to 1.6b include minor bug fixes, a VMS
makefile that has been tested and works, a new '-n' option to specify
the use of a DNA matrix for comparisons, and a new -x option that
allows you to specify positive or negative offsets in the alignment
numbering. I have been using the latter option to compare promoters,
lalign -x "-604 -942" gene1.seq gene2.seq
allows me to do a local sequence comparison and have residue 1
correspond to the start of transcription in both sequences. This
option can also be handy for formatting sequences for publication. The
option has been tested extensively, but may still have a bug or two.
In addition, the documentation has been extensively revised.
There is now a file, fasta16.me, designed to be printed by
nroff/troff/psroff -me that explains the changes, installation, and
use of FASTA in much more detail.
The 1.6b release of FASTA for the IBM-PC is also available for
$60.00 prepaid, $85.00 with a purchase order, $10.00 for overseas
shipping. This is the first new IBM-PC release since 1.4d, and has
many new options and new programs, including SSEARCH (rigorous
Smith-Waterman alignment), LALIGN (rigorous local alignments), and
PLALIGN (plots of local alignments). I hope to have new version of
these programs for the Macintosh by March 1; it is will be available
for the same price as the IBM-PC/DOS versions.
wrp at virginia.EDU