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 e.g. in plastids. The software was used to obtain the results described in [1–4].
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 the GNU General Public License (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 | |
References
- 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 The Fifth Congress of Vavilov society of geneticists and breeders, 2009, June 21-27, Moscow, Part II, p. 68. (in Russian)
- 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)
- V.A. Lyubetsky, O.A. Zverkov, L.I. Rubanov, A.V. Seliverstov. Modeling RNA polymerase competition: the effect of σ-subunit knockout and heat shock on gene transcription level. Biology Direct, 2011, Vol. 6, Art. 3. DOI: 10.1186/1745-6150-6-3
- V.A. Lyubetsky, O.A. Zverkov, S.A. Pirogov, L.I. Rubanov, A.V. Seliverstov. Modeling RNA polymerase interaction in mitochondria of chordates. Biology Direct, 2012, Vol. 7, Art. 26. DOI: 10.1186/1745-6150-7-26