FASTA program discussion list

[William Pearson <>]

A new release of the FASTA programs, fasta-36.3.5b, is available from:

http://faculty.virginia.edu/wrpearson/fasta/fasta36/fasta-36.3.5b.tar.gz

In addition, a windows version of the program is available from:

http://faculty.virginia.edu/wrpearson/fasta/fasta36/fasta-36.3.5b.zip

This is a bug-fix version of fasta-36.3.5a, which addresses the following 
problems:

(1) The MPI version now compiles and runs.  Unfortunately, the current MPI 
version is much less efficient than the threaded versions; the threaded 
versions have considerably lower communications overhead.

(2) Problems with DNA matrices specified as files, e.g. -s ../data/dna.mat, 
have been fixed.

(3) A major improvement in fasta-36.3.5 is the ability to keep the library in 
memory for searches with multiple queries. However, this dramatically 
increased the memory footprint, particularly if memory mapped NCBI databases 
were searched. fasta-36.3.5b is much more aggressive about releasing memory 
mapped files, and closing NCBI auxiliary files, so that the program can run 
in smaller memory environments.

(4) A problem with negative scan times has been fixed.

(5) Some problems with statistical estimates with DNA sequence searches have 
been fixed.

(6) A problem that limited the maximum length of a protein query sequence has 
been fixed (it is still MAXLIB_P=36000).

(7) The logic for the -b '=50', -b '>50' has been fixed, particularly for the 
case where statistical estimates are not calculated.

As always, please let me know about bugs as you encounter them.

Bill Pearson