bwGRID

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Rosetta

What is Fasta?

Das FASTA-Format ist ein textbasiertes Format zur Darstellung und Speicherung der Primärstruktur von Nukleinsäuren (Nukleinsäuresequenz) und Proteinen (Proteinsequenz) in der Bioinformatik. Die Nukleinbasen bzw. Aminosäuren werden durch einen Ein-Buchstaben-Code dargestellt. Das Format erlaubt es, den Sequenzen einen Namen und Kommentare voranzustellen.

This is the version 36 of the FASTA program package (see W. R. Pearson and D. J. Lipman (1988), “Improved Tools for Biological Sequence Analysis”, PNAS 85:2444-2448, [16] W. R. Pearson (1996) “Effective protein sequence comparison” Meth. Enzymol. 266:227- 258 [14]; and Pearson et. al. (1997) Genomics 46:24-36 [17].

This is the first MPI version of Fasta.

Version 3 of the FASTA packages contains many programs for searching DNA and protein databases and for evaluating statistical
significance from randomly shuffled sequFALSE"

Fasta Software is free for academic and non-profit users.

URL: UVA Fasta Server - Download and Documentation

Download Fasta and License Information

Fasta Software is free for academic and non-profit users.

If you want to use Fasta on our bwGRID-HPC-System, please

... contact us using this email : rainer.rutka(at)uni-konstanz.de

... we will then contact the user with instructions for using CPMD on our cluster.

  • Fasta Latest Distribution : the actual distribution of Rosetta we are running is: 36.3.5b

    Installed programs (in /opt/bwgrid/chem/fasta/36.3.5b/bin):

    1. fasta36 (main programm)
      fasta36_mpi
    2. fastf36
      fastf36_mpi
    3. fastm36
      fastm36_mpi
    4. fasts36
      fasts36_mpi
    5. fastx36
      fastx36_mpi
    6. fasty36
      fasty36_mpi
    7. ggsearch36
      ggsearch36_mpi
    8. glsearch36
      glsearch36_mpi
    9. reln.sh (create symbolic link omitting '_mpi')
    10. ssearch36
      ssearch36_mpi
    11. tfastf36
      tfastf36_mpi
    12. tfasts36
      tfasts36_mpi
    13. tfastx36
      tfastx36_mpi
    14. tfasty36
      tfasty36_mpi

    blue = symbolic links

bwGRID Anpassungen / adaptations

bwGRID-Setups

Fasta

Description: Configuration - Makefile
Path/Filename: /opt/bwgrid/chem/fasta/36.3.5b/make/Makefile.mpi_icc_sse2
Description: Module - File
Path/Filename: /opt/bwgrid/chem/fasta/36.3.5b/modulefiles/chem-fasta-36.3.5b
ALL-IN-ONE: TGZ - Tarball | expand in /opt/bwgrid/chem/fasta/36.3.5b with [tar xvzf]
Path/Filename: /opt/bwgrid/chem/fasta/36.3.5b/fasta36.3.5b-bwgridconfig.tgz

Build Fasta parallel mode

...
cd ../src
# ignore performance warnings (see above)
make -f ../make/Makefile.mpi_icc_sse2
...

(see Modules-File)

bwGRID examples

The PBS batch system can be used to manage the nodes allocation in a cluster of hosts. For example, using a particular job script, it's possible to communicate to the MPI launcher program (mpirun) the number and the list of nodes that PBS has allocated for the whole job as requested from the user. The PBS server will not run more jobs on the busy nodes until the end of the current job. Here is an example of a script to do this over our bwGRID network using an implementation of Open-MPI.

Description: bwGRID - Example PBS File for submitting a job via. 'qsub'
Path/Filename: /opt/bwgrid/chem/fasta/36.3.5b/bwgrid-examples/bw-grid-fasta36-example.pbs
Description: Database file for bwgrid example. Copy into $FASTAHOME/conf folder
Path/Filename: /opt/bwgrid/chem/fasta/36.3.5b/bwgrid-examples/bwgrid_e
ALL-IN-ONE: TGZ - Tarball | expand in /opt/bwgrid/chem/fasta/36.3.5b - folder with [tar xvzf]
Path/Filename: /opt/bwgrid/chem/fasta/36.3.5b/fasta36-bwgridexamples.tgz

© Copyright 1988, 1991, 1992, 1993, 1994 1995, 2011 by William R. Pearson and the University of Virginia.
Δ 14.12.2011 | initial version | rainer.rutka(at)uni-konstanz.de