April 9, 2008

The FASTA programs for Windows32 environments (WindowsNT, 2000, XP)
has undergone a major upgrade, so that now all the programs in the
Unix/MacOSX distribution are available to Windows users.  Moreover,
Windows users with modern (SSE2 compatible) processors can run greatly
accelerated versions of the Smith-Waterman ssearch program.

The Windows program set now matches version 35 of Unix/MacOSX program
set.

Moreover, these programs work both with FASTA formatted files, and
NCBI BLAST formatted files.

The following programs are available:

    fasta35.exe	       	protein-protein or DNA-DNA database searches
    fastf35.exe
    fastm35.exe
    fasts35.exe
    fastx35.exe		compare DNA query to protein library with frameshifts
    fasty35.exe		compare DNA query to protein library with frameshifts
    ggsearch35.exe	global-global protein-protein or DNA-DNA
    glsearch35.exe	global-local protein-protein or DNA-DNA
    lalign35.exe	multiple non-overlapping local alignments
    ssearch35.exe	Smith-Waterman for prot-prot or DNA-DNA searches
    ssearch35sse2.exe	Smith-Waterman, accelerated with SSE2 extensions
    tfastf35.exe
    tfastm35.exe
    tfasts35.exe
    tfastx35.exe	compare protein to DNA library with frameshifts
    tfasty35.exe	compare protein to DNA library with frameshifts

Each of these programs also has a "threaded" version, which can run on
multiple processors (or dual cores) if they are available.  However,
to run multiple threads, you must download the pthreadVC2.dll that provides
pthreads functions from:

ftp://sources.redhat.com/pub/pthreads-win32/dll-latest/lib/pthreadVC2.dll

see also http://sourceware.org/pthreads-win32/

Without that DLL, the program will not run at all. The current
compilation supports two threads, and speeds up searches about 2-fold
on dual-core processors.

    fasta35_t.exe
    fastf35_t.exe
    fastm35_t.exe
    fasts35_t.exe
    fastx35_t.exe
    fasty35_t.exe
    ggsearch35_t.exe
    glsearch35_t.exe
    ssearch35sse2_t.exe
    tfastf35_t.exe
    tfasts35_t.exe
    tfastx35_t.exe
    tfasty35_t.exe

If you do not have multiple processors, you do not need to worry about
these programs or the pthreads library.

The programs have been tested with protein and DNA databases in FASTA
format, PIR/GCG-text format, and Genbank flatfile format.  The program
does not work properly with GCG binary format databases, but it seems
unlikely that Windows users would need these. 

Be certain to use an program that can work with long file names when
unpacking the program source files.

Please report bugs to:

	wrp@virginia.edu