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.

Snippy 4.6.0 – Find SNPs/indels in a Bacterial Genome from NGS reads

Snippy 4.6.0

:: 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

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl
bwa mem
samtools
awk

:: DOWNLOAD

Snippy

:: MORE INFORMATION

Wombac 2.1 – Bacterial core Genome SNPs for Phylogenomic Trees from NGS Reads and/or draft genomes

Wombac 2.1

:: DESCRIPTION

Wombac rapidly finds core genome SNPs from samples and produces an alignment of those SNPs which can be used to build a phylogenomic tree.

::DEVELOPER

Torsten Seemann

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl
bwa mem
samtools

:: DOWNLOAD

Wombac

:: MORE INFORMATION

EPIGPUHSIC 1.0 – Compute HSIC between all possible interaction of SNPs and a Quantitative Phenotype

EPIGPUHSIC 1.0

:: DESCRIPTION

EPIGPUHSIC is an approach to epistasis detection by exhaustive testing of all possible SNP pairs. The search strategy based on the Hilbert-Schmidt Independence Criterion can help delineate various forms of statistical dependence between the genetic markers and the phenotype.

::DEVELOPER

Bertram Mueller-Myhsok (bmm@mpipsykl.mpg.de) & Tony Kam-Thong [tony@mpipsykl.mpg.de], Machine Learning and Computational Biology Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
R package
gputools R package
CUDA developer driver and Toolkit
GENABLE

:: DOWNLOAD

EPIGPUHSIC

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jul 1;27(13):i214-21. doi: 10.1093/bioinformatics/btr218.
Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs.
Kam-Thong T, Pütz B, Karbalai N, Müller-Myhsok B, Borgwardt K.

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

Precision Medicine Genomics Laboratory

:: 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.

snpEnrichR – Automating Enrichment analysis of GWAS SNPs

snpEnrichR

:: DESCRIPTION

snpEnrichR is an R package to analyze co-localization of SNPs and their proxies in genomic regions

::DEVELOPER

Computational systems biology group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
R

:: DOWNLOAD

snpEnrichR

:: MORE INFORMATION

Citation

Bioinformatics, 34 (23), 4112-4114 2018 Dec 1
snpEnrichR: Analyzing Co-Localization of SNPs and Their Proxies in Genomic Regions
Kari Nousiainen , et al.

FamLBL 1.0 – Detecting Rare Haplotype Disease Association Based on Common SNPs Using Case-Parent Triads

FamLBL 1.0

:: DESCRIPTION

famLBL (family-triad-based logistic Bayesian Lasso) is an R package for estimating effects of haplotypes on complex diseases using SNP data.

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
R package

:: DOWNLOAD

FamLBL

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 21. pii: btu347. [Epub ahead of print]
FamLBL: Detecting Rare Haplotype Disease Association Based on Common SNPs Using Case-Parent Triads.
Wang M1, Lin S2.

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

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.