BACH / BACH-MIX – Bayesian 3D constructor for Hi-C data / Characterize Structural Variations of Chromatin Folding

BACH / BACH-MIX

:: DESCRIPTION

BACH is a novel Bayesian probabilistic approach for analyzing Hi-C data. BACH takes the Hi-C contact matrix and local genomic features (restriction enzyme cutting frequencies, GC content and sequence uniqueness) as input and produces, via MCMC computation, the posterior distribution of three-dimensional (3D) chromosomal structure

BACH-MIX is an extended BACH algorithm to characterize structural variations of chromatin folding

::DEVELOPER

Jun Liu

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux
R

:: DOWNLOAD

BACH , BACH-MIX

:: MORE INFORMATION

Citation

Hu M, Deng K, Qin Z, Dixon J, Selvaraj S, Fang J, Ren B, Liu JS. (2013)
Bayesian Inference of Spatial Organizations of Chromosomes.
PLoS Computational Biology 9(1): e1002893.

BACH – Gene Composer

BACH

:: DESCRIPTION

Bach is a gene composer software that optimizes coding sequences and calculates corresponding RiPS to illustrate their translation rates. In sequence optimization, Bach incorporates 4 distinct approaches from which users can freely choose: SYNONYMOUS SUBSTITUTION, SLOW, FAST and MATCH. In the last section of GET RIPS, users are provided with a quantitative view of the translational behavior of the input coding sequence and the four sequences produced by the four methods as well.

::DEVELOPER

Wendy (Chenyu) Hu wendyhu001@gmail.com; @ Zhejiang University

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

BACH

:: MORE INFORMATION

BACH 1.1 – Fast Haplotype Inference via Context Tree Weighting

BACH 1.1

:: DESCRIPTION

BACH (BAyesian context-based Haplotype inference) solves so-called genotype phasing (or haplotype inference) problem. It is based on Bayesian approach to model haplotypes and genotypes with variable order Markov chains. It finds accurate haplotypes for given genotypes by Bayesian maximum a posterior criterion.

::DEVELOPER

Pasi Rastas

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux /MacOsX
Java

:: DOWNLOAD

BACH

:: MORE INFORMATION

Citation

Pasi Rastas, Jussi Kollin, Mikko Koivisto
Fast Bayesian Haplotype Inference via Context Tree Weighting
K. Crandall, J. Lagergren (Eds.), Proc. 8th Workshop on Algorithms in Bioinformatics – WABI 2008, pp. 259-270.