**Changes with release 20u5 - May 1996

This version of the FASTA package includes FASTX - a program that
compares a DNA sequence with a protein sequence library by translating
the DNA sequence in three frames and finding the best match, with
frame-shifts, between the translated DNA and protein sequence.
(unlike BLASTX, FASTX only does a three-frame translation.  To search
all six frames, do a second search with the "-i" option).

The code for aligning a three-frame protein sequence with a normal
protein sequence was provided by Zheng Zhang and W. Miller of the
Pennsylvania State University.

A third gap parameter, the frameshifts penalty, is provided with the
'-h' option.  The default gap penalties are -15 for the first residue
in a gap, -3 for each additional residue, and -30 for a frameshift.

The '-h' option used to prevent the histogram display, that option is
now invoked with '-H'.

Much of the FASTX code is new and has not been tested nearly as
extensively as the other fasta programs. Please inform me of bugs as
you find them.

================
**Changes with release 20u51 - June, 1996

Fixes to showalign for SHOWALL.

Fixes to routines that read fasta format files for long DNA sequences.

================
**Changes with release 20u52 - July, 1996

Fixes to lalign/plalign for setting gap penalties on DNA

Fixes to fastx to correct bug in alignment routine.

================
**Changes with release 20u53 - July, 1996

Another fix to fastx 

Added flalign, a version of plalign that produces a GCG fig file for
local aligment graphics.

Increased the size of sequences that can be aligned by lalign to
120,000 residues with BIGMEM.

First release of Mac version with FASTX.

================

Bill Pearson
wrp@virginia.edu