Tag: SNP

AffyMAPSDetector 1.0 – Affymetrix MicroArray Probe SNP Detector

AffyMAPSDetector 1.0

:: DESCRIPTION

 AffyMAPSDetector stands for Affymetrix MicroArray Probe SNP Detector. It detects the presence of SNPs (Single Nucleotide Polymorphism) in the probes of Affymetrix GeneChipTM expression arrays. However, it can be used to characterize any GeneChipTM with respect to SNPs for which NCBI fully supports gene and SNP annotations (i.e. the organism for which GeneChipTM is desinged and that organism’s genome exists in NCBI nucleotide and SNP database).

DEVELOPER

AffyMAPSDetector Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 AffyMAPSDetector

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Jul 30;8:276.
AffyMAPSDetector: a software tool to characterize Affymetrix GeneChip expression arrays with respect to SNPs.
Kumari S, Verma LK, Weller JW.

GenoSNP 1.3 – SNP Genotyping

GenoSNP 1.3

:: DESCRIPTION

GenoSNP is a genotyping algorithm for the Illumina Infinium SNP genotyping assay [1]. It is entirely within-sample and does not require the need for a population of control samples nor parameters derived from such a population. The ability to call genotypes using only within-sample information makes the method computationally light and practical for studies involving rare variants and small sample sizes.

::DEVELOPER

Eleni Giannoulatou at eleni@well.ox.ac.uk

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • C Compiler

:: DOWNLOAD

 GenoSNP

:: MORE INFORMATION

Citation

A Variational Bayes within-sample SNP genotyping algorithm that does not require a reference population.
Giannoulatou E, Yau C, Colella S, Ragoussis J, Holmes CC.
Bioinformatics. 2008 Oct 1;24(19):2209-14

 

SNP2CAPS – SNP and INDEL Analysis Tool for CAPS Marker Development

SNP2CAPS

:: DESCRIPTION

SNP2CAPS facilitates the computational conversion of SNPs into CAPS markers. A simple algorithm involves the screening of multiply-aligned sequences for restriction sites followed by a selection pipeline that allows the deduction of CAPS candidates by the identification of putative alternative restriction sites.

::DEVELOPER

Thomas Thiel  at the IPK-Gatersleben

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Perl

:: DOWNLOAD

 SNP2CAPS

:: MORE INFORMATION

Citation

T. Thiel, R. Kota, I. Grosse, N. Stein, and A. Graner.
SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development.
Nucleic Acids Research, 32(1):e5, 2004.

SNP HiTLink 1.5.1 – SNP High-Throughput Linkage Analysis System

SNP HiTLink 1.5.1

:: DESCRIPTION

SNP HiTLink (SNP High-Throughput Linkage Analysis System)is a computer program providing a useful pipeline to directly connect SNP (Single Nucleotide Polymorphism) data and linkage analysis program.

::DEVELOPER

Dynacom

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
:: DOWNLOAD

 SNP HiTLink

:: MORE INFORMATION

Citation

Fukuda Y, Nakahara Y, Date H, Takahashi Y, Goto J, Miyashita A, Kuwano R, Adachi H, Nakamura E, Tsuji S.
SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data.
BMC Bioinformatics. 2009 Apr 24;10(1):121.

SNPALYZE 8.0 – SNP and Disease Association Analysis Software

SNPALYZE 8.0

:: DESCRIPTION

SNPAlyze is able to import many specific types of Genotyping data files and analyze them.When case-control studies are analyzed, in addition to the columns with genotyping data, extra columns for cases and controls are necessary in order to distinguish the groups.

::DEVELOPER

Dynacom

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
:: DOWNLOAD

  SNPALYZE

:: MORE INFORMATION

Citation

Shimo-Onoda, Tanaka, Furushima, Nakajima, Toh, Harata, Yone, Komiya, Adachi, Nakamura, Fujimiya, Inoue(2002),
“Akaike’s information criterion for a measure of linkage disequilibrium“,
J Hum Genet, 47(12): 649-655

mPopTag – Multi-Population Tag SNP Picker

mPopTag

:: DESCRIPTION

mPopTag (Multi-Population Tag SNP Picker) is a tool used to select or evaluate linkage disequilibrium (LD) tag SNPs for multiple populations. The program analyzes patterns of LD–measured by composite linkage disequilibrium (CLD) or r2–between polymorphic sites in a genome region for multiple populations. It also uses an agreedy algorithm to select a single set of near-minimum numbers of LD tag SNPs for multiple populations.

::DEVELOPER

Jack A. Taylor, M.D., Ph.D. , Zongli Xu, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 mPopTag

:: MORE INFORMATION

Citation:

Xu Z, Kaplan NL, Taylor JA.
Tag SNP selection for candidate gene association studies using HapMap and gene resequencing data.
Eur J Hum Genet 2007 Oct;15(10):1063-70.

AsVis 20051125 – Visualizing Association Rules in SNP Neighborhoods

AsVis 20051125

:: DESCRIPTION

AsVis is a web application for visualizing association rules obtained from short, sequential data (such as SNP neighborhoods) by means of data mining. It allows the association rules to be sorted by a variety of measures and filtered by position, enabling fast, interactive data exploration.

::DEVELOPER

Group of Data mining in genetics 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Web Server
  • CGI

:: DOWNLOAD

 AsVis

:: MORE INFORMATION

Citation

Kimmo Kulovesi et al
Visualisation of Associations Between Nucleotides in SNP Neighbourhoods
Workshop on Intelligent Data Analysis in bioMedicine and Pharmacology (IDAMAP’06), Verona, Italy, August 2006.

Clarki 20090715 – Use SNP data for Species Identification

Clarki 20090715

:: DESCRIPTION

Clarki estimate the composition of hybrids using SNP and other diallelic loci that have fixed differences between taxa.

::DEVELOPER

Steven Kalinowski, Ph.D.

:: SCREENSHOTS

::REQUIREMENTS

:: DOWNLOAD

 Clarki

:: MORE INFORMATION

Citation

Kalinowski ST (2009)
How to uses SNPs and other diagnotic diallelic genetic markers to estimate the composition of multi-species hybrids.
Conservation Genetics Resources, Volume 2, Number 1, December 2010 , pp. 63-66(4)

CLUSTAG – Hierarchical Clustering and Graph Methods for Selecting Tag SNPs

CLUSTAG

:: DESCRIPTION

CLUSTAG is a software of hierarchical clustering and graph methods for selecting tag SNPs

CLUSTAG Online Version

::DEVELOPER

Michael Kwok-Po Ng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • Java
:: DOWNLOAD

 CLUSTAG

:: MORE INFORMATION

Citation

Ao, S.I., Kevin Yip, Michael K. Ng, David Cheung, Pui-Yee Fong, Ian Melhado and Pak C Sham (2005)
CLUSTAG: Hierarchical Clustering and Graph Methods for Selecting Tag SNPs.
Bioinformatics. v21(8), 1735-1736.

ATRIUM 1.0 – Testing Untyped SNPs in Case-Control Association Studies with Related Individuals

ATRIUM 1.0

:: DESCRIPTION

ATRIUM is a C++ program that performs case-control association testing between a binary trait and an untyped SNP, based on genotype data from multiple typed SNPs that are in linkage disequilibrium with the untyped SNP, where information on the joint distribution of typed and untyped SNPs is obtained from an external reference panel. A special feature of ATRIUM is that both related and unrelated individuals can be included in the case-control sample. The user specifies a set of untyped SNPs on which external reference panel information is available, and the ATRIUM program computes a test statistic for association with each untyped SNP in the set. This test is suitable for case-control analysis in any outbred sample with related and/or unrelated individuals, including large pedigrees, provided that the relationships are known.

::DEVELOPER

Zuoheng Wang and Mary Sara McPeek

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • C Compier

:: DOWNLOAD

 ATRIUM

:: MORE INFORMATION

Citation

Wang, Z., and McPeek, M.S. (2009).

ATRIUM: Testing untyped SNPs in case-control association studies with related individuals.
Am. J.Hum. Genet. 85, 667-678.