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Nucleosomes Position Prediction by Genomic Sequence


You can generate the nucleosomes positioning predictions on your own machine using our executable and wrapping Perl scripts below.

NOTE:THIS SOFTWARE IS FREELY AVAILABLE FOR ACADEMIC USE ONLY, and is distributed under the The GNU Lesser General Public License.


Requirements

  1. The executable is compiled both for 32 bit and 64 bit Linux machines. It is wrapped by Perl scripts.
  2. The executable uses Xerces, a third party shared library. You can find its license terms at http://www.apache.org/licenses/LICENSE-2.0.

Download Instructions

  1. Select one of the available versions (we highly recommend the most recenet one, Version 3, see below), and download the 64 bit or the 32 bit archive file into a folder of your choice.
  2. Unzip and extract its content (e.g. tar xvfz 64bit_exe_nucleosome_prediction.tar.gz).
  3. Type make install

Usage


The main script is nucleosome_prediction.pl, type: nucleosome_prediction.pl --help to see its usage.

The script can work in two modes:

Output Probabilities

In this mode, which is the default one, the output contains the probability of a nucleosome to start at each basepair and the average occupancy per basepair.
The download zip file contains example files:
  • input.fa - input fasta file
  • occ_output.tab - output tab delimited file
  • occ_output.gxp - output gxp file (Genomica project file).
See below the command that produced these output files on each executable version.

Output Log-Ratio Binding

To generate the raw nucleosome binding log-ratio per basepair, add -raw_binding to the parameters.
The download zip file contains example files:
  • input.fa - input fasta file
  • raw_output.tab - output tab delimited file
  • raw_output.gxp - output gxp file (Genomica project file).
See below the command that produced these output files on each executable version.




Version 3 - December 2008



General Information

This version is based on Kaplan et al., "The DNA-Encoded Nucleosome Organization of a Eukaryotic Genome", Nature 2008.
There is a single available model in this version, and it is applicable for all the species.

Examples

The example output files were produced by these command lines:
Output probabilities mode: ./nucleosome_prediction.pl -t Example -s input.fa -p occ_output -tab -gxp
Output Log-Ratio Binding mode: ./nucleosome_prediction.pl -t Example -s input.fa -p raw_output -tab -gxp -raw_binding


Download


64 bit version
32 bit version



Version 2 - September 2008



General Information

This version is based on Field et al., "Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals", PLoS Comp Biol 2008.
There is a single available model in this version, and it is applicable for all the species.

Examples

The example output files were produced by these command lines:
Output probabilities mode: ./nucleosome_prediction.pl -t Example -s input.fa -p occ_output -tab -gxp
Output Log-Ratio Binding mode: ./nucleosome_prediction.pl -t Example -s input.fa -p raw_output -tab -gxp -raw_binding


Download


64 bit version
32 bit version


Version 1 - July 2006



General Information

This version is based on Segal et al, "A Genomic Code for Nucleosome Positioning", Nature 2006.
There are two available models in this version, one learnt from yeast data and one from chicken.

Examples

The example output files were produced by these command lines:
Output probabilities mode: ./nucleosome_prediction.pl -t Example -m models/yeast_center_avg3_bck_ds.gxw -s input.fa -p occ_output -tab -gxp
Output Log-Ratio Binding mode: ./nucleosome_prediction.pl -t Example -m models/yeast_center_avg3_bck_ds.gxw -s input.fa -p raw_output -tab -gxp -raw_binding


Download


Only a 32 bit version is available, 64 bit machines can execute this version too.
32 bit version


For troubleshooting and FAQ please visit our executables FAQ page.