FASTA program discussion list

[William Pearson <>]

The latest version of the FASTA package, fasta-36.3.4, is available from:

http://faculty.virginia.edu/wrpearson/fasta/fasta36/fasta-36.3.4.tar.gz

This version provides a number of significant changes in the user interface.

(1) By default, the FASTA programs are no longer interactive.  Typing:

        fasta36

provides a brief help display:

% fasta36
USAGE
 fasta36 [-options] query_file library_file [ktup]
 fasta36 -help for a complete option list

DESCRIPTION
 FASTA searches a protein or DNA sequence data bank
 version: 36.3.4 Mar, 2011

COMMON OPTIONS (options must preceed query_file library_file)
 -s:  [BL50] scoring matrix;
 -f:  [-10] gap-open penalty;
 -g:  [-2] gap-extension penalty;
 -S   filter lowercase (seg) residues;
 -b:  high scores reported (limited by -E by default);
 -d:  number of alignments shown (limited by -E by default);
 -I   interactive mode;

To use the older interactive mode, use fasta36 -I.

(2) The fasta36_t (*_t) threaded versions are no longer named *_t; fasta36 
(and ssearch36, fastx36, etc) are threaded by default on Unix/Linux/MacOSX 
systems (there is no longer a fasta36 and fasta36_t, only fasta36).

(3) The programs no longer show the histogram by default.  The meaning of the 
-H option is reversed (and consistent with fasta36_mpi)

(4) Documentation is substantially improved.  See doc/fasta_guide.pdf.

(5) A number of BLAST compatible output formats are available.  -m BB tries 
to imitate BLAST completely.

As always, let me know about bugs.

Bill Pearson