08:38:55
Laboratory of Mathematic methods and models in bioinformatics,
Institute for Information Transmission Problems,
Russian Academy of Sciences
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].
[1] 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)
[2] O.A. Zverkov, A.V. Seliverstov, L.I. Rubanov, V.A. Lyubetsky. Modeling of RNA polymerases competition: influence of the sigma subunit knockout and of the temperature on genes expression // "Information Technologies and Systems": Proc. of Conf. ITaS'32, Bekasovo (Moscow Region), December 15-18, 2009, p. 328-331. (in Russian)
[3] Lyubetsky V.A., Zverkov O.A., Rubanov L.I., Seliverstov A.V. Modeling RNA polymerase competition: the effect of sigma-subunit knockout and heat shock on gene transcription level // Biology Direct, 2011, 6:3. http://www.biology-direct.com/content/6/1/3
[4] Lyubetsky V.A., Zverkov O.A., Pirogov S.A., Rubanov L.I., Seliverstov A.V. Modeling RNA polymerase interaction in mitochondria of chordates // Biology Direct, 2012, 7:26. http://www.biology-direct.com/content/7/1/26
The software is available in two flawors:
Rivals - the graphical application (Windows executable)
cpRivals - the portable command line utility for MPI-based multiprocessing (Windows binaries and Linux source code freely available under GNU GPL) 
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.
Downloadable files
| 32-bit | 64-bit | |
| Readme | ||
| User's Manual (pdf) - in Russian | 2.0 | |
| Rivals executable for Windows with .NET 2.0 | 1.5.3.3 | --- |
| cpRivals executables for Windows without MPI | 1.5.3.3 | 1.5.3.3 |
| cpRivals executables for Windows with MPICH2 1.4.1p installed | 1.5.3.3 | 1.5.3.3 |
| Microsoft VC++ redistributable libraries | 9.0.30729.4148 | 9.0.30729.4148 |
| MPICH2 implementation of the MPI-2 standard for Windows (by Argonne National Laboratory) | 1.4.1p1 | 1.4.1p1 |
| cpRivals source code for Linux - GNU GPL V3 | 1.5.3.3a | |