snpEff 4.3T – Variant Annotation and Effect Prediction Tool

snpEff 4.3T

:: DESCRIPTION

snpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes).

SnpSift is a collection of tools to manipulate VCF (variant call format) files.

SnpEffWrapper takes a VCF and applies Annotations from a GFF using SnpEff

::DEVELOPER

snpEff team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

snpEff / SnpEffWrapper

:: MORE INFORMATION

Citation

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.
Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM.
Fly (Austin). 2012 Apr-Jun;6(2):80-92.

Indelz 0.1 – Predict the Effects of Indels and non-sense Mutations

Indelz 0.1

:: DESCRIPTION

Indelz is bioinformatics method to predict the effects of indels and non-sense mutations Link to software.

::DEVELOPER

Alan Moses’ Computational Biology Lab ,University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Indelz

:: MORE INFORMATION

Citation

Ranking insertion, deletion and nonsense mutations based on their effect on genetic information
Amin Zia, Alan M Moses
BMC Bioinformatics. 2011; 12: 299.

OEFinder 0.0.2 – Identify Ordering Effect Genes in Single Cell RNA-seq data

OEFinder 0.0.2

:: DESCRIPTION

OEFinder is a user interface to identify and visualize ordering effects in single-cell RNA-seq data.

::DEVELOPER

Ning Leng

:: SCREENSHOTS

OEFinder

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 OEFinder

:: MORE INFORMATION

Citation

OEFinder: A user interface to identify and visualize ordering effects in single-cell RNA-seq data.
Leng N, Choi J, Chu LF, Thomson JA, Kendziorski C, Stewart R.
Bioinformatics. 2016 Jan 6. pii: btw004.

MLSTA – Machine Learning Integration for Predicting the Effect of Single Amino Acid Substitutions on Protein Stability

MLSTA

:: DESCRIPTION

MLSTA is a machine learning integration for predicting the effect of single amino acid substitutions on protein stability.

::DEVELOPER

Polymer Research Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Struct Biol. 2009 Oct 19;9:66. doi: 10.1186/1472-6807-9-66.
Machine learning integration for predicting the effect of single amino acid substitutions on protein stability.
Ozen A1, Gönen M, Alpaydan E, Haliloğlu T.

B-NEM – Boolean Nested Effect Models

B-NEM

:: DESCRIPTION

B-NEM combines the use of downstream effects with the higher resolution of signalling pathway structures in Boolean Networks.

::DEVELOPER

B-NEM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

 B-NEM

:: MORE INFORMATION

Citation

Analyzing synergistic and non-synergistic interactions in signalling pathways using Boolean Nested Effect Models.
Pirkl M, Hand E, Kube D, Spang R.
Bioinformatics. 2015 Nov 17. pii: btv680.

ENCoM – Exploring Protein Conformational Space and Effect of Mutations on Protein Function and Stability

ENCoM

:: DESCRIPTION

ENCoM is a coarse grained normal modes analysis method to evaluate thermostability of proteins.

::DEVELOPER

Najmanovich Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ENCoM

:: MORE INFORMATION

Citation

ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability.
Frappier V, Chartier M, Najmanovich RJ.
Nucleic Acids Res. 2015 Apr 16. pii: gkv343.

mCSM – Predicting Effect of Mutations in Proteins using Graph-based Signatures

mCSM

:: DESCRIPTION

mCSM is a novel approach to the study of missense mutations which relies on graph-based signatures.

::DEVELOPER

Douglas Eduardo Valente Pires 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

mCSM: predicting the effects of mutations in proteins using graph-based signatures.
Pires DE, Ascher DB, Blundell TL.
Bioinformatics. 2014 Feb 1;30(3):335-42. doi: 10.1093/bioinformatics/btt691.

PROVEAN 1.1.5 – Protein Variation Effect Analyzer

PROVEAN 1.1.5

:: DESCRIPTION

PROVEAN is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.

::DEVELOPER

PROVEAN Team, J. Craig Venter Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PROVEAN

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Apr 6. pii: btv195.
PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels.
Choi Y, P Chan A

PLoS One. 2012;7(10):e46688. doi: 10.1371/journal.pone.0046688. Epub 2012 Oct 8.
Predicting the functional effect of amino acid substitutions and indels.
Choi Y, Sims GE, Murphy S, Miller JR, Chan AP.

BAMSE – Bayesian Association for Multiple SNP Effects

BAMSE

:: DESCRIPTION

BAMSE is a software for performing association studies of multiple SNPs and environmental factors.

::DEVELOPER

BAMSE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • C++ Compiler

:: DOWNLOAD

 BAMSE

:: MORE INFORMATION

EFFECT 2013 – Automated Construction and Extraction of Features for Classification of Biological Sequences

EFFECT 2013

:: DESCRIPTION

EFFECT is an algorithmic framework for automated detection of functional signals in biological sequences.

::DEVELOPER

Computational Biology lab, George Mason University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • BioJava

:: DOWNLOAD

 EFFECT

:: MORE INFORMATION

Citation

Uday Kamath, Kenneth A. De Jong, and Amarda Shehu.
“Effective Automated Feature Construction and Selectionfor Classification of Biological Sequences.”
PLoS One, 2014 (in press).