McPromoter 006 – The Markov Chain Promoter Prediction Server

McPromoter 006

:: DESCRIPTION

McPromoter is a program aiming at the exact localization of eukaryotic RNA polymerase II transcription start sites.

::DEVELOPER

Uwe Ohler’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Genome Biol. 2002;3(12):RESEARCH0087. Epub 2002 Dec 20.
Computational analysis of core promoters in the Drosophila genome.
Ohler U, Liao GC, Niemann H, Rubin GM.

MCPD 2.02 – Markov Chain Pooling Decoder

MCPD 2.02

:: DESCRIPTION

MCPD is used in the analyis of pooling experiments for library screening. Pools are collections of clones, and screening a pool with a probe is a group test, determining whether any of these clones are positive for the probe. The results of the pool screenings are interpreted, or decoded, to infer which clones are candidates to be positive using a Markov chain Monte Carlo approach. MCPD implements this MCMC to compute marginal probabilities of clones using a Bayesian model for the experiment

::DEVELOPER

Alexander Schliep’s group for bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C Compiler

:: DOWNLOAD

MCPD

:: MORE INFORMATION

Citation

J Comput Biol. 1996 Fall;3(3):395-406.
Interpretation of pooling experiments using the Markov chain Monte Carlo method.
Knill E, Schliep A, Torney DC.

 

HMC 0.9.1 – Haplotype Inference tool based on Markov Chain model

HMC 0.9.1

:: DESCRIPTION

HMC (Haplotype Inference Based on Markov Chain)is a new haplotype inference methods based on Markov chain model which do not assume haplotype blocks in the population and allows each individual haplotype to have its own structure, thus are able to accommodate recombination and obtain higher adaptivity to the genotype data, specifically in the case of long marker maps. The proposed method presents a general Markov chain model for haplotype inference problem. A dynamic programming algorithm is developed for the model. The algorithm is theoretically guaranteed to find exact global optimal solutions within polynomial running time. Through extensive computational experiments on simulated and real genotype data, the designed algorithm is shown to be efficient, and outperforms previous methods.

::DEVELOPER

APORC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  HMC

:: MORE INFORMATION

Citation

Ling-Yun Wu, Ji-Hong Zhang, and Raymond Chan.
Improved approach for haplotype inference based on Markov chain.
In Proceedings of 2nd International Symposium on Optimization and Systems Biology, Lecture Notes in Operations Research, Vol. 9, pp. 204–215, World Publishing Corporation, Beijing, 2008.

 

GFMCMC 1.0 – C Library of GLUT for Markov Chain Monte Carlo

GFMCMC 1.0

:: DESCRIPTION

GFMCMC (GLUT for Markov Chain Monte Carlo) This is a library of C code that I wrote to use the (relatively) platform-independent OpenGL Utilities Toolkit (GLUT) for rendering pictures of one’s MCMC simulation in real time. It is essentially a small application programming interface.

::DEVELOPER

Eric C. Anderson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • C Compiler

:: DOWNLOAD

 GFMCMC

:: MORE INFORMATION