3 The FASTA programs for Windows32 environments (WindowsNT, 2000, XP)
4 has undergone a major upgrade, so that now all the programs in the
5 Unix/MacOSX distribution are available to Windows users. Moreover,
6 Windows users with modern (SSE2 compatible) processors can run greatly
7 accelerated versions of the Smith-Waterman ssearch program.
9 Moreover, these programs work both with FASTA formatted files, and
10 NCBI BLAST formatted files.
12 The following programs are available:
14 fasta34.exe protein-protein or DNA-DNA database searches
18 fastx34.exe compare DNA query to protein library with frameshifts
19 fasty34.exe compare DNA query to protein library with frameshifts
21 prss34.exe evaluate statistical significance using shuffles
23 ssearch34.exe Smith-Waterman for prot-prot or DNA-DNA searches
24 ssearch34sse2.exe Smith-Waterman, accelerated with SSE2 extensions
28 tfastx34.exe compare protein to DNA library with frameshifts
29 tfasty34.exe compare protein to DNA library with frameshifts
31 Each of these programs also has a "threaded" version, which can run on
32 multiple processors (or dual cores) if they are available. However,
33 they are built using the Unix pthreads API, so to use these programs,
34 you must download the pthreadVC2.dll from:
36 ftp://sources.redhat.com/pub/pthreads-win32/dll-latest/lib/pthreadVC2.dll
38 see also http://sourceware.org/pthreads-win32/
56 Without that DLL, the threaded programs will not run at all. The
57 current compilation supports two threads, and speeds up searches about
58 2-fold on dual-core processors.
60 The programs have been tested with protein and DNA databases in FASTA
61 format, PIR/GCG-text format, and Genbank flatfile format. The program
62 does not work properly with GCG binary format databases, but it seems
63 unlikely that Windows users would need these.
65 Be certain to use an program that can work with long file names when
66 unpacking the program source files.
68 Please report bugs to: