nsSNPAnalyzer – Predicting Disease-associated Nonsynonymous Single Nucleotide Polymorphisms

nsSNPAnalyzer

:: DESCRIPTION

nsSNPAnalyzer is a web tool to predict whether a nonsynonymous single nucleotide polymorphism (nsSNP) has a deleterious effect. nsSNPAnalyzer extracts structural and evolutionary information from a query nsSNP and uses a machine learning method called Random Forest to predict the nsSNP’s phenotypic effect.

::DEVELOPER

Yan Cui’s Lab at University of Tennessee Health Science Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W480-2.
nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms.
Bao L, Zhou M, Cui Y.

EFIN – Evaluation of Functional Impact of Nonsynonymous SNPs

EFIN

:: DESCRIPTION

EFIN is a free tool which predict whether amino acids substitution would related to disease evaluated by random forests based on protein conservation.

::DEVELOPER

WANLING YANG’S GROUP IN BIOINFORMATICS @ University of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Jun 10;15:455. doi: 10.1186/1471-2164-15-455.
EFIN: predicting the functional impact of nonsynonymous single nucleotide polymorphisms in human genome.
Zeng S, Yang J, Chung BH, Lau YL, Yang W

Syn-SCAN 0.9 – Synonymous Nonsynonymous Mutation Rates between Sequences Containing Ambiguous Nucleotides

Syn-SCAN 0.9

:: DESCRIPTION

Syn-SCAN calculates the synonymous and nonsynonmous mutation rates between sequences containing ambiguous nucleotides

::DEVELOPER

Stanford HIVDB Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
Perl

:: DOWNLOAD

Syn-SCAN

:: MORE INFORMATION

Citation

Synonymous-non-synonymous mutation rates between sequences containing ambiguous nucleotides (Syn-SCAN).
Gonzales MJ, Dugan JM, Shafer RW.
Bioinformatics. 2002 Jun;18(6):886-7.

BN-BS – Estimation of Synonymous and Nonsynonymous Branch Lengths from Pairwise Distances

BN-BS

:: DESCRIPTION

BN-BS is a software to estimate branch lengths in terms of synonymous and nonsynonymous substitutions per site, while the tree topology is given. The program uses the modified Nei-Gojobori method (Zhang et al. 1998) to estimate pairwise synonymous and nonsynonymous distances among present-sequences and then estimates branch lengths and their variances by using the ordinary least-squares method.

::DEVELOPER

Jianzhi Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

BN-BS

:: MORE INFORMATION

Citation:

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