SNPSpD / SNPSpDlite – Single Nucleotide Polymorphism Spectral Decomposition

SNPSpD / SNPSpDlite

:: DESCRIPTION

SNPSpD is a method of correcting for non-independence of SNPs in LD with each other

SNPSpDlite takes the same input at SNPSpD, but ONLY outputs the LD correlation matrix, Meff and MeffLi estimates and GOLD input (i.e., does not perform time-consuming varimax/promax rotations) thus allowing users to obtain Meff/MeffLi values for large numbers (1000s) of SNPs.

::DEVELOPER

the Statistical and Genomic Epidemiology Laboratory (SGEL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Am J Hum Genet. 2004 Apr;74(4):765-9. Epub 2004 Mar 2.
A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequilibrium with each other.
Nyholt DR.

remuRNA – Measurement of Single-Nucleotide Polymorphism-induced Changes of RNA Conformation

remuRNA

:: DESCRIPTION

remuRNA commutes the relative entropy between the Boltzmann ensembles of the native and a mutant structure.

::DEVELOPER

Teresa Przytycka Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
C Compiler

:: DOWNLOAD

remuRNA

:: MORE INFORMATION

Citation

Detecting SNP-induced structural changes in RNA: application to disease studies.
Salari R, Kimchi-Sarfaty C, Gottesman M, Przytycka TM.
Nucleic Acids Reserarch (RECOMB 2012)

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.

multiPopTagSelect 1.1 – Select Tagging Single-nucleotide Polymorphisms

multiPopTagSelect 1.1

:: DESCRIPTION

multiPopTagSelect attempts to select a near-minimal set of tagging single-nucleotide polymorphisms (tagSNPs) that account for all observed patterns of linkage disequilibrium (LD) in multiple populations. Specifically, it processes the output of tagSNP selection algorithms that designate bins of nearly equivalent SNPs, such that choosing (and typing) one SNP from each bin is sufficient to capture all associations observed in the data. Most of this documentation concerns one particular tagSNP selection method known as ldSelect, but multiPopTagSelect can also be used with other methods whose output has been converted into ldSelect format. This program can optimize SNP selection across any number of populations, and it can be applied to genomic regions ranging from small genes to entire chromosomes.

::DEVELOPER

Dr. Deborah Nickerson’s lab at the University of Washington

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / Max OS X
Perl

:: DOWNLOAD

multiPopTagSelect

:: MORE INFORMATION

Citation

Howie BN, Carlson CS, Rieder MJ, Nickerson DA. Efficient selection of tagging single-nucleotide polymorphisms in multiple populations. Hum Genet. 2006 120(1):58-68.