| Hilfe-Text | This is the MPI version of Fasta!
DESCRIPTION
Release 3.6 of the FASTA package provides a modular set of sequence
comparison programs that can run on conventional single processor
computers or in parallel on multiprocessor computers. More than a dozen
programs are currently available (see FASTA AT A GLANCE).
All the comparison programs share a set of basic command line options;
additional options are available for individual comparison functions.
Threaded versions of the FASTA programs run in parallel on modern
Linux and Unix multi-core or multi-processor computers.
Accelerated versions of the Smith-Waterman algorithm are available
for architectures with the Intel SSE2 or Altivec PowerPC architectures,
which can speed-up Smith-Waterman calculations 10 - 20-fold.
On this cluster, only the MPI parallel versions are available such as
fasta36_mpi, ssearch36_mpi, fastx36_mpi, etc..
The MPI parallel versions use the same command line options as the
serial and threaded versions.
FASTA AT A GLANCE
/opt/bwhpc/common/bio/fasta/36.3.8/bin
* fasta36(_mpi) - scan a protein or DNA sequence library for similar sequences
* fastx36(_mpi) - compare a DNA sequence to a protein sequence database,
comparing the translated DNA sequence in forward and reverse frames.
* tfastx36(_mpi) - compare a protein sequence to a DNA sequence database,
calculating similarities with frameshifts to the forward and reverse
orientations.
* fasty36(_mpi) - compare a DNA sequence to a protein sequence database,
comparing the translated DNA sequence in forward and reverse frames.
* tfasty36(_mpi) - compare a protein sequence to a DNA sequence database,
calculating similarities with frameshifts to the forward and reverse
orientations.
* fasts36(_mpi) - compare unordered peptides to a protein sequence database.
* fastm36(_mpi) - compare ordered peptides (or short DNA sequences) to a
protein (DNA) sequence database.
* tfasts36(_mpi) - compare unordered peptides to a translated DNA sequence
database.
* fastf36(_mpi) - compare mixed peptides to a protein sequence database.
* tfastf36(_mpi) - compare mixed peptides to a translated DNA sequence
database.
* ssearch36(_mpi) - compare a protein or DNA sequence to a sequence database
using the Smith-Waterman algorithm.
* ggsearch36(_mpi) - compare a protein or DNA sequence to a sequence database
using a global alignment (Needleman-Wunsch).
* glsearch36(_mpi) - compare a protein or DNA sequence to a sequence database
with alignments that are global in the query and local in the database
sequence (global-local).
* lalign36(_mpi) - produce multiple non-overlapping alignments for protein and
DNA sequences using the Huang and Miller sim algorithm for the Water-
man-Eggert algorithm.
* prss36, prfx36 - discontinued; all the FASTA programs will estimate
statistical significance using 500 shuffled sequence scores if two
sequences are compared.
This version is compiled with openmpi support synced Intel- and System-
Math-Libraries.
DOCUMENTATION
* Get started:
http://fasta.bioch.virginia.edu/fasta_www2/fasta_intro.shtml
German - https://de.wikipedia.org/wiki/FASTA-Format
English - https://en.wikipedia.org/wiki/FASTA_format
* Fasta Sequence Comparison at the U. of Virginia:
http://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml
* Full manual, command-line optionen and more:
/opt/bwhpc/common/bio/fasta/36.3.8/doc
http://fasta.bioch.virginia.edu/fasta_www2/fasta_guide.pdf
http://www.genome.jp/tools-bin/show_man?fasta
http://home.cc.umanitoba.ca/~psgendb/birchhomedir/doc/fasta/fasta36.1.html
* Fasta tests can be found here:
/opt/bwhpc/common/bio/fasta/36.3.8/examples
/opt/bwhpc/common/bio/fasta/36.3.8/test
* bwHPC examples and a moab example script can be found here:
/opt/bwhpc/common/bio/fasta/36.3.8/bwhpc-examples
CITATION
Code in the smith_waterman_sse2.c and smith_waterman_sse2.h files
is copyright (c) 2006 by Michael Farrar. Code in the
global_sse2.c, global_sse2.h, glocal_sse2.c, and glocal_sse2.h
files is copyright (c) 2010 by Michael Farrar.
In case of problems, please contact: bwhpc (at) uni-konstanz.de
This module is available for all users. |