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Kategorie/Name/Versionbio/fasta/36.3.8
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conflict bio/fasta
LizenzApache License [http://www.apache.org/licenses/LICENSE-2.0]
URL http://faculty.virginia.edu/wrpearson/
What-isbio/fasta/36.3.8 : Fasta36.3.8 Scan a protein or DNA sequence library for similar sequences
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.
SupportbwHPC Support-Portal
Installationsdatum05.10.2017
Löschdatum
Best-Practice-Wikihttp://www.bwhpc-c5.de/wiki/index.php/Fasta