Tag: SNP

ABACUS 1.0 – Identify SNPs Significantly Associated with a Disease within predefined sets of SNPs

ABACUS 1.0

:: DESCRIPTION

ABACUS (Algorithm based on a BivAriate CUmulative Statistic) is designed to identify SNPs significantly associated with a disease within predefined sets of SNPs such as pathways or genomic regions.Applied to a whole SNP dataset, ABACUS gives as output a list of SNP-sets associated with the disease and, for each SNP-set, the list of significant SNPs. ABACUS is robust to the concurrent presence of SNPs with protective and detrimental effects and of common and rare variants; moreover it is powerful even when few SNPs in the SNP-set are associated with the phenotype.

::DEVELOPER

SYSTEMS BIOLOGY AND BIOINFORMATICS GROUP

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • R package

:: DOWNLOAD

 ABACUS

:: MORE INFORMATION

Citation

Di Camillo B, Sambo F, Toffolo G, Cobelli C.
ABACUS: an entropy based cumulative bivariate statistic robust to rare variants and different direction of genotype effect .
Bioinformatics. 2014 Feb 1;30(3):384-91. doi: 10.1093/bioinformatics/btt697.

SNPack 1.0 – Compression and fast Retrieval of SNP data

SNPack 1.0

:: DESCRIPTION

SNPack is a novel algorithm and file format for compressing and retrieving SNP data, specifically designed for large-scale association studies.

::DEVELOPER

SYSTEMS BIOLOGY AND BIOINFORMATICS GROUP

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 SNPack

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jul 26. pii: btu495.
Compression and fast retrieval of SNP data.
Sambo F, Di Camillo B, Toffolo G, Cobelli C.

csnpAnalysis 1.01 – PANTHER Coding SNP Analysis tool

csnpAnalysis 1.01

:: DESCRIPTION

 csnpAnalysis is a software to estimate the likelihood that a particular nonsynonymous (amino-acid changing) coding SNP will cause a functional impact to the protein.

::DEVELOPER

Paul D. Thomas

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 csnpAnalysis

:: MORE INFORMATION

Citation

Paul D. Thomas, et al. 2006.
Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools.
Nucl. Acids Res.34: W645-W650.

PSM – Pyrogram SNP Miner

PSM

:: DESCRIPTION

PSM Uses PyrosequencingTM to identify de novo SNPs in pooled DNA samples

::DEVELOPER

Yeong-Shin Lin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Mar;39(5):e28. doi: 10.1093/nar/gkq1249. Epub 2010 Dec 3.
A simple method using PyrosequencingTM to identify de novo SNPs in pooled DNA samples.
Lin YS1, Liu FG, Wang TY, Pan CT, Chang WT, Li WH.

snpQC – Quality Control of Illumina SNP Genotyping Array data

snpQC

:: DESCRIPTION

snpQC is an R based fully automated pipeline for preprocessing, storage and quality control of Illumina SNP data.

::DEVELOPER

Cedric Gondro

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux / MacOsX/ Windows
  • R

:: DOWNLOAD

  snpQC

:: MORE INFORMATION

Citation

Anim Genet. 2014 Oct;45(5):758-61. doi: 10.1111/age.12198. Epub 2014 Jul 18.
SNPQC–an R pipeline for quality control of Illumina SNP genotyping array data.
Gondro C1, Porto-Neto LR, Lee SH.

SNPlice 1.8.0 – Find SNPs influencing splicing in NGS mRNA data

SNPlice 1.8.0

:: DESCRIPTION

SNPlice is a software tool to find and evaluate the co-occurrence of single-nucleotide-polymorphisms (SNP) and altered splicing in next-gen mRNA sequence reads.

::DEVELOPER

The Horvath Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 SNPlice

:: MORE INFORMATION

Citation

SNPlice: Variants that Modulate Intron-retention from RNA-sequencing Data.
Mudvari P, Movassagh M, Kowsari K, Seyfi A, Kokkinaki M, Edwards NJ, Golestaneh N, Horvath A.
Bioinformatics. 2014 Dec 6. pii: btu804

PEAS 1.0 – Package for Elementary Analysis of SNP data

PEAS 1.0

:: DESCRIPTION

The goal of PEAS is to provide the average user who is working on SNP data the basic analysis tools, and make it possible to analysis large SNP data set for those people who do not write programs. PEAS focus on population genetic analysis of SNP data and most commonly used SNP data operations.

::DEVELOPER

Population Genomics Group (PGG)

:: SCREENSHOTS

PEAS

:: REQUIREMENTS

  • Windows
  • .net

:: DOWNLOAD

 PEAS

:: MORE INFORMATION

Citation

Mol Ecol Resour. 2010 Nov;10(6):1085-1088. doi: 10.1111/j.1755-0998.2010.02862.x.
PEAS V1.0: a package for elementary analysis of SNP data.
Xu S, Gupta S, Jin L.

VIP 1.0 – SNP Variant Detection tool from Pooled DNAs

VIP 1.0

:: DESCRIPTION

VIP (Variant Identification by Pooling)is a complete data analysis framework for  overlapping pool design. It is very flexible and can be combined with any pool design approaches and sequence mapping/alignment tools.

::DEVELOPER

Computational Biology lab @ Case (CBC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Perl
  • MatLab

:: DOWNLOAD

 VIP

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jan 1;29(1):29-38. doi: 10.1093/bioinformatics/bts645. Epub 2012 Oct 27.
Rare variant discovery and calling by sequencing pooled samples with overlaps.
Wang W1, Yin X, Soo Pyon Y, Hayes M, Li J.

HREfinder 1.0 – Detection of Homologous Recombination Events from SNP data

HREfinder 1.0

:: DESCRIPTION

The HREfinder is a software for predicting homologous recombination events (HREs) in a set of whole genomes

::DEVELOPER

HREfinder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 HREfinder

:: MORE INFORMATION

Citation

PLoS One. 2013 Oct 7;8(10):e75230. doi: 10.1371/journal.pone.0075230. eCollection 2013.
Detection of homologous recombination events in bacterial genomes.
Wang WB1, Jiang T, Gardner S.

diSNPselection – Disease Informative SNP Selection for Gene-based Association tests

diSNPselection

:: DESCRIPTION

diSNPselection is a Matlab code for disease informative SNP (diSNP) selection for gene-based association tests.

::DEVELOPER

Yuehua Cui, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • MatLab

:: DOWNLOAD

 diSNPselection

:: MORE INFORMATION

Citation:

Brief Bioinform. 2014 Mar;15(2):279-91. doi: 10.1093/bib/bbs087. Epub 2013 Jan 15.
Boosting signals in gene-based association studies via efficient SNP selection.
Wu C1, Cui Y.