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 BIOINFORMATICSUniversity of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: 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

KisSplice 2.4.0-p1 – Local Transcriptome Assembler for SNPs and AS events

KisSplice 2.4.0-p1

:: DESCRIPTION

KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler, which enables to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number of biological conditions, and will quantify each variant in each condition. It has been tested on Illumina datasets of up to 300M reads.

::DEVELOPER

KisSplice Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac OS X /  Linux

:: DOWNLOAD

 KisSplice

:: MORE INFORMATION

Citation

Gustavo AT Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot, Pierre Peterlongo and Vincent Lacroix,
KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.
BMC Bioinformatics 2012, 13(Suppl 6):S5

PPFS 2 – Add on to kSNP for predicting Phenotypes from SNPs in Microbial Genome

PPFS 2

:: DESCRIPTION

The PPFS (Predict Phenotypes From SNPs) package is an add-on to kSNP , a program that can identify SNPs in a data set of hundreds of microbial genomes.

::DEVELOPER

Barry G. Hall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

PPFS

:: MORE INFORMATION

Citation

PLoS One. 2014 Feb 28;9(2):e90490. doi: 10.1371/journal.pone.0090490. eCollection 2014.
SNP-associations and phenotype predictions from hundreds of microbial genomes without genome alignments.
Hall BG1.

SnpTracker 0.1 – Extract the latest version rsID and Genomic Coordinates of SNPs given any version of rs ID(s)

SnpTracker 0.1

:: DESCRIPTION

SnpTracker is a small tool to extract the latest version rsID and genomic coordinates of SNPs given any version of rs ID(s)

::DEVELOPER

Miao-xin Li, The University of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 SnpTracker

:: MORE INFORMATION

Citation

SNPTracker: A Swift Tool for Comprehensive Tracking and Unifying dbSNP rsIDs and Genomic Coordinates of Massive Sequence Variants.
Deng JE, Sham PC, Li MX.
G3 (Bethesda). 2015 Nov 19. pii: g3.115.021832. doi: 10.1534/g3.115.021832.

Snippy 3.0 – Find SNPs/indels in a Bacterial Genome from NGS reads

Snippy 3.0

:: DESCRIPTION

Snippy finds SNPs between a haploid reference genome and your NGS sequence reads (handles reads >500bp long). It will find both substitutions and insertions/deletions (indels).

::DEVELOPER

Torsten Seemann <torsten.seemann@monash.edu>,Victorian Bioinformatics Consortium

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • bwa mem
  • samtools
  • awk

:: DOWNLOAD

 Snippy

:: MORE INFORMATION

SNPExpress 1.00 – Interrogation of the localized effects of common SNPs on Exon and Transcript level Expression

SNPExpress 1.00

:: DESCRIPTION

SNPExpress is a database interface that we developed to permit interrogation of the effects of common SNPs on exon and transcript level expression. This database enables researchers to input a SNP, gene, or a genomic region to investigate regions of interest for localized effects of SNPs on exon and gene level expression changes.

::DEVELOPER

SNPExpress team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 SNPExpress

:: MORE INFORMATION

Citation

PLoS Biol. 2008 Dec 23;6(12):e1.
Tissue-specific genetic control of splicing: implications for the study of complex traits.
Heinzen EL, Ge D, Cronin KD, Maia JM, Shianna KV, Gabriel WN, Welsh-Bohmer KA, Hulette CM, Denny TN, Goldstein DB.

BALL-SNP – Combining Genetic and Structural Information to Identify Candidate Non-synonymous SNPs

BALL-SNP

:: DESCRIPTION

BALL-SNPgp is the extension of the proof-of-concept tool BALL-SNP, a software tool based on the Biochemical Algorithms Library (BALL), a molecular modeling framework, providing robust and sophisticated algorithms on structural bioinformatics. BALL-SNPgp enables the assessment of multiple non-synonymous single nucleotide polymorphisms (nsSNPs) in a single protein by visualizing the mutated residues within the wild type structure, collecting available pathogenicity information from different databases, predicting binding pockets, protein stability changes and pathogenicity, as well as performing a cluster analysis on comprised amino acid substitutions

::DEVELOPER

Chair for clinical bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • BALL

:: DOWNLOAD

 BALL-SNPgp

:: MORE INFORMATION

Citation:

BALL-SNP: combining genetic and structural information to identify candidate non-synonymous single nucleotide polymorphisms.
Mueller SC, Backes C, Kalinina OV, Meder B, Stöckel D, Lenhof HP, Meese E, Keller A.
Genome Med. 2015 Jul 1;7(1):65. doi: 10.1186/s13073-015-0190-y.

JEPEG 0.2.0 / JEPEGMIX 0.1.0 – Joint Effect on Phenotype of eQTLs/functional SNPs associated with a Gene

JEPEG 0.2.0 /JEPEGMIX 0.1.0

:: DESCRIPTION

JEPEG is a novel software which uses only summary statistics and correlation structures estimated from a reference popluation, to i) impute the summary statistics at unmeasured eQTLs and ii) test for the joint effect of measured and imputed all eQTLs affecting a gene function/expression on a phenotype.

JEPEGMIX is a JEPEG extension for gene-level joint testing of functional variants.

::DEVELOPER

dleelab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 JEPEG , JEPEGMIX

:: MORE INFORMATION

Citation

JEPEGMIX: gene-level joint analysis of functional SNPs in cosmopolitan cohorts.
Lee D, Williamson VS, Bigdeli TB, Riley BP, Webb BT, Fanous AH, Kendler KS, Vladimirov VI, Bacanu SA.
Bioinformatics. 2015 Oct 1. pii: btv567

JEPEG: a summary statistics based tool for gene-level joint testing of functional variants.
Lee D, Williamson VS, Bigdeli TB, Riley BP, Fanous AH, Vladimirov VI, Bacanu SA.
Bioinformatics. 2014 Dec 12. pii: btu816

Chi8 v1 – GPU program for Detecting Significant Interacting SNPs with the Chi-square 8-df test

Chi8 v1

:: DESCRIPTION

Chi8 is a program that calculates the chi-square 8 degree of freedom test between all pairs of SNPs in a brute force manner on a Graphics Processing Unit.
Usman Roshan

::DEVELOPER

Usman Roshan

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Chi8

:: MORE INFORMATION

Citation

Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test.
Al-Jouie A, Esfandiari M, Ramakrishnan S, Roshan U.
BMC Res Notes. 2015 Sep 14;8:436. doi: 10.1186/s13104-015-1392-5.

FunciSNP 1.10.0 – Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs

FunciSNP 1.10.0

:: DESCRIPTION

FunciSNP integrates information from GWAS, 1000genomes and chromatin feature to identify functional SNP in coding or non-coding regions.

::DEVELOPER

FunciSNP  team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 FunciSNP

:: MORE INFORMATION

Citation

FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs.
Coetzee SG, Rhie SK, Berman BP, Coetzee GA, Noushmehr H.
Nucleic Acids Res. 2012 Oct;40(18):e139. doi: 10.1093/nar/gks542.