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Furthermore, randomized versions of the applied databases were appended to the original databases using the decoy perl script (Matrix Science, Boston, USA) downloadable at.
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A custom Perl script, matrix-bidirectional.pl, was run against mouse chromosome files available from Ensemble (version NCBIM37.49) ftp://ftp.ensembl.org/pub/current_fasta/mus_musculus/dna/ (see Additional file 1) [ 34].
This was converted to an ordered matrix of homology groups within the contigs using custom python and R scripts.
40068_2014_31_MOESM1_ESM.doc Additional file 1: R script for matrix normalization.
The tired gender script in The Matrix isn't due to the fact that the Wachowskis are transgender women.
The respective R script for automatic matrix normalisation and combination is provided in the online supporting information (Additional file 1).
The R script for automatic matrix normalization and combination provided herein can be a useful tool for future ecosystem monitoring in freshwater, marine and terrestrial systems.
The created dta files were then merged using the merge script tool from Matrix Science (http://www.matrixscience.com).com
The numbers of read tags aligning to each region were summarized using a custom python script producing a matrix of counts (tags per region per sample).
The numbers of read tags aligning to each gene were extracted using a custom python script producing a matrix of counts with regions based on the Ensembl transcript annotation (version 66).
Proteome clustering results and matrix, scripts, and sequences alignments are available from GitHub (https://github.com/ocisse/Pneumocystis_comparative, last accessed July 27 , 2014.
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