Recently, several bugs in the FASTA package have been fixed
and a new version is avaiable via anonymous ftp from:
(1) Code has been included to allow the EMBL and PIR CD-ROM's to be
read on unix systems. Because these CD-ROM's include a <CR><LF>
character but unix expects a <LF> end of line, sequence annotations were
sometimes garbled. Hopefully this has been fixed.
(2) A bug in RDF2 has been fixed. When comparing DNA sequences, RDF2
used an incorrect scoring method for initial regions. RDF2 worked
properly on protein sequences. RDF2 does work properly on DNA sequences
if the "-k" option is used. This problem was discovered because the
unshuffled scores for RDF2 were different from the FASTA scores for many
DNA sequences. This should not happen; if you find examples with the new
version of RDF2, please contact me.
In addition, a bug in the Mac FASTA version 1.6c2 has been reported.
Code that was included in the Mac 1.4x version to allow the EMBL
CD-ROM to be read properly was omitted from the 1.6 version. As a
result, MacFASTA does not read properly the sequence files (either
EMBL or PIR format) from the EMBL CD-ROM. It will also not read other
CD-ROM formats properly. I hope to send out corrected versions of
MacFASTA 1.6c this weekend or early next week.
The CD-ROM problem does not affect DOS versions; the RDF2 problem is
present in DOS and Macintosh versions.
The Macintosh and DOS versions are not available via anonymous FTP.