BM-DE 2 – Bayesian Method of Calling Differential Expression

BM-DE 2

:: DESCRIPTION

BMDE is a Bayesian hierarchical model for the inference on the differential gene expression based on RNA-Seq data

::DEVELOPER

Yuan Ji Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package

:: DOWNLOAD

 BM-DE

 :: MORE INFORMATION

Citation

Cancer Inform. 2011;10:205-15. doi: 10.4137/CIN.S7473. Epub 2011 Aug 1.
On differential gene expression using RNA-Seq data.
Lee J1, Ji Y, Liang S, Cai G, Müller P.

BM-BC 1.0 – Bayesian method of Base Calling for Solexa Sequence data

BM-BC 1.0

:: DESCRIPTION

BM-BC is a Bayesian method of base calling for Solexa-GA sequencing data. The Bayesian method builds on a hierarchical model that accounts for three sources of noise in the data, which are known to affect the accuracy of the base calls: fading, phasing, and cross-talk between channels.

::DEVELOPER

Yuan Ji Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package

:: DOWNLOAD

 BM-BC

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012;13 Suppl 13:S6. doi: 10.1186/1471-2105-13-S13-S6. Epub 2012 Aug 24.
BM-BC: a Bayesian method of base calling for Solexa sequence data.
Ji Y, Mitra R, Quintana F, Jara A, Mueller P, Liu P, Lu Y, Liang S.

ngLOC 1.0 – Bayesian method for Predicting Protein Subcellular Localization

ngLOC 1.0

:: DESCRIPTION

ngLOC is an n-gram-based Bayesian classifier that predicts subcellular localization of proteins both in prokaryotes and eukaryotes. The overall prediction accuracy varies from 85.3% to 91.4% across species.

::DEVELOPER

Guda Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • C++ Compiler

:: DOWNLOAD

 ngLOC

:: MORE INFORMATION

Citation

ngLOC: software and web server for predicting protein subcellular localization in prokaryotes and eukaryotes.
King BR, Vural S, Pandey S, Barteau A, Guda C.
BMC Res Notes. 2012 Jul 10;5:351. doi: 10.1186/1756-0500-5-351.

Ancestor – Inference of Ancestral Amino Acid Sequences by the Distance-Based Bayesian Method

Ancestor

:: DESCRIPTION

Ancestor is a software which infer ancestral amino acid sequences from a set of homologous amino acid sequences whose phylogenetic relationships are known.

::DEVELOPER

Jianzhi Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  Ancestor

:: MORE INFORMATION

Citation:

Zhang J, Nei M (1997)
Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods.
J Mol Evol 44(Suppl 1):S139-S146

Anc-gene – Inference of Ancestral Gene Sequences by the Distance-Based Bayesian Method

Anc-gene

:: DESCRIPTION

Anc-gene is a software for inference of ancestral nucleotide sequences of protein coding genes from a set of present-day sequences whose phylogenetic relationships are known. It first infers the amino acids by the distance-based Bayesian method, and then infers the underlying nucleotide sequences by fixing the inferred amino acids.

::DEVELOPER

Jianzhi Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Anc-gene

:: MORE INFORMATION

Citation:

Zhang J, Rosenberg HF, Nei M (1998)
Positive Darwinian selection after gene duplication in primate ribonuclease genes.
Proc. Natl. Acad. Sci. USA 95:3708-3713.