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The MATLAB script (Source code 1) has been updated to avoid any ambiguity.
For Tyr1P sorting, an in-house script (Source code 1) was used as described previously in Fenouil et al. (2012).
Tile scans were acquired of 25 fields, and cells were outlined manually using a custom built MatLab script (Source code 1).
Wiggle files scores were retrieved with an in-house R script (Source code 1) for hg19 Refseq annotations and coordinates defined for selected enhancers and promoters.
With an in-house script (Source code 1), the positions of motifs were converted to GFF formatted files taking into account the positions of Refseq hg19 annotations.
Finally, another in-house script (Source code 1) converted those GFF to a binary matrix that was output in a format readable by Java Treeview software.
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A PDP is an archive containing a plan file together with application content files such as web archives, database schemas, scripts, source code, localization bundles, icons etc.
Further analysis and data display was performed using custom designed Matlab scripts (Source code 1).
Data were analyzed using custom Perl and Matlab (Mathworks, Natick, MA, United States) scripts (Source code 1), which conform to the open source definition.
The primary tool of the Biogem framework is a software generator consisting of templates for bioinformatics scripts, source code, software specification, documentation and tests.
ROI summary statistics, including pattern similarity estimates, were extracted with in-house scripts (Source code 1) in MATLAB 2009b (The MathWorks, Inc., Natick, MA), and statistical comparisons were conducted in R version 3.1.1 (http://www.R-project.org).org
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