Laboratory of Mathematic methods and models in bioinformatics,
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Software for modeling of RNA polymerase competition
The software is intended for modeling of the competition of RNA polymerases which are transcribing genes in different DNA strands. This regulation mechanism occurs in plant and alga organelles eg. in plastids. With use of the software we obtained the results described in [1-4].
 V.A. Lyubetsky, L.I. Rubanov, A.V. Seliverstov. Competition of RNA polymerases which transcribe common locus in opposed directions // Congress of geneticists and breeders on the occasion of Darvin's 200th anniversary and Fifth Congress of Vavilov society of geneticists and breeders, 2009, June 21-27, Moscow, Part II, p. 68. (in Russian)
The software is available in two flawors:
Both options inplement the same algorithm and use compatible data files, but differ in functions and performance. Rivals application is primarily for the source data files preparation, in-process monitoring and preliminary experiments. cpRivals utility is intended for mass processing on high-performance clusters.
Starting from version 1.5.x.x, both programs provide direct support of circular gene sequences and dynamic modification of parameters within a model trajectory. Starting from version 1.5.3.x, the programs' performance dramatically increase.