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Home >> Research >> Bioinformatics
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SOMBRERO

SOMBRERO Download

SOMBRERO v.1.1 is now available for download. See below for a summary of changes in this update of the software. The software is free to use, on condition that any use of the software in a publication will be acknowledged by citation of the relevant publications. Note that this software is still very much under construction, so please contact the author with any bugs or problems (shaun.mahony(AT)nuigalway.ie).

Binaries: Precompiled binaries for various systems are available below. If your system does not appear in the list, try compiling the source yourself or otherwise contact the author.

Backgrounds: The "BackExtract.pl" perl script included in the SOMBRERO release allows the user to create their own background model for any organism. The following frequently requested background files are provided for the user's convenience:
backgrounds.zip: This zip file contains 3rd-order Markov models of intergenic DNA for the genomes of E. coli, S. cerevisae, Drosophila and Human. The human background may be suitable for other mammalian genomes, but if in doubt, generate your own background.

Priors: Pre-trained binding profile SOMs for use with the "-prior" option in SOMBRERO. At the moment, users cannot train their own binding profile SOMs, and only the list below is supported. All suggestions of other sources for binding matrix datasets would be greatly appreciated.

SOM Prior Files Created Using Clusterings Files
(includes pretrained SOMs of various sizes for use with the "-prior" option)   (Lists positions of training PSSMs on SOM. Do not use the below files with SOMBRERO!)
Mammalian Priors Mammalian & JASPAR PSSMs Clusterings
Drosophila Priors Pollard Dataset Clusterings
Yeast Priors SCPD Clusterings
TRANSFAC Priors TRANSFAC 7.4 Clusterings

Source Code: SOMBRERO is released under the GNU General Public Licence. The source code for SOMBRERO is available from this link, but no guarantees are offered as to the code's stability or even if the code will compile on the user's system. Note that the "ftime" timing function is deprecated on some systems. If you are getting errors related to ftime, please use this version of the code instead.

Parallelised SOMBRERO Source: A parallelised version of SOMBRERO has been written using MPI. The source code is available from this link, but again, we cannot guarantee whether or not the code will compile/run on the user's system. This version of SOMBRERO must be run using "mpirun", e.g. "mpirun -np 4 ./SOMBRERO" or sometimes "mpirun -np 4 -machinefile $PBS_NODEFILE ./SOMBRERO", where -np specifies the number of processors to use. Please talk with your system's administrator about using an MPI program on the multi-processor system.

Changes in version 1.1:

  • Support for including information on known transcription factor binding matrices in the initialisation.
  • Support for masking lowercase characters and N's.
  • The size of the SOM is by default chosen automatically according to the size of the input dataset.
  • Complexity threshold can now be adjusted.
  • Entirely random initialisation now allowed.
  • Error in the SOMBRERO Viewer fixed.
  • Other minor bugs fixed.



Department of Information Technology,
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Phone: +353 (0)91 524411 ext 3549, E-mail: aaron.golden(AT)nuigalway.ie
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