$Id: fasta_versions.html 256 2010-03-29 13:41:48Z wrp $
| Version | New Programs | Other changes |
|---|---|---|
| fasta-36 | None |
The major improvement in FASTA v36 is the ability to calculate and
display multiple significant alignments (multiple HSP's) between a
query sequence and a library sequence. Previous FASTA versions had
the serious shortcoming of only showing the best
alignment. A tfastx36 alignment between a protein and its
exon-containing gene will show all of the exon alignments that are
long enough to be significant.
FASTA v36 also provides more flexible strategies for searching lists of datbase files, and versions after fasta-36.2 are fully threaded, so both searches and alignments can be distributed among multiple processors with efficient speedup. PVM/MPI parallel versions of FASTA v36 are under development. |
| fasta-35 | +lalign35+ggsearch35+glsearch35-prss3-prfx3
|
FASTA v35 provides significant improvements in statistical accuracy and program efficiency in threaded (multi-CPU, multi-core) environments. The program now automatically produces 500 random shuffles when small libraries are searched. Thus, prss and prfx are no longer required; ssearch35 and fastx35 provide the same function. |
| fasta34 | +ssearch3+fasts3/tfasts3+fastf3/tfastf3-lfasta-lalign-tfasta
|
FASTA v34 is the last version of the FASTA3 series before the
significant changes introduced with FASTA v35. The FASTA v3
programs were first introduced in 1996, with threaded code
for multi-processors, more accurate statistical estimates, and
optimal Smith-Waterman alignments with ssearch. More
recent versions (v34) provided accelerated Smith-Waterman searches
using Altivec and SSE2 vector processors. FASTA v34 is no longer
updated for bug fixes. |
| fasta2 | +lfasta+tfasta
|
FASTA v2 was introduced in 1995, improving sensitivity by
calculated gapped alignment scores. Modern (V34 and V35) versions of
FASTA have significantly more robust statistical estimates, threaded
code, and vectorized Smith-Waterman, so FASTA v2 should not be used
for database searching. However, until lalign was addeed
to FASTA v35 in March, 2007, FASTA v2 was the only source for
the lalign program. Today, the only programs provided in
FASTA v2 that are not provided in FASTA v35 are the Kyte-Doolittle
hydropathy plotter grease and the classic (though very
inaccurate) secondary structure prediction programs chofas
and garnier |