Tag: Mutation

Prethermut 3.1 – Predicting Changes in Protein Thermostability brought about by Single- or Multi-site Mutations

Prethermut 3.1

:: DESCRIPTION

Prethermut is a method to identify the effect of single- or multi-site mutations on protein thermostability based on machine learning methods.

::DEVELOPER

Biotechnology Research Institute, Chinese Academy of Agricultural Sciences

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 Prethermut

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Jul 2;11:370. doi: 10.1186/1471-2105-11-370.
Predicting changes in protein thermostability brought about by single- or multi-site mutations.
Tian J1, Wu N, Chu X, Fan Y.

PATHiVar – Assessing Functional Impact of Mutations over Human Signalling Network

PATHiVar

:: DESCRIPTION

PATHiVar is a web-based tool that integrates genomic variation data with gene expression tissue information.

::DEVELOPER

Computational Genomics Department ,Principe Felipe Research Center, Valencia, Spain

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Assessing the impact of mutations found in next generation sequencing data over human signaling pathways.
Hernansaiz-Ballesteros RD, Salavert F, Sebastián-León P, Alemán A, Medina I, Dopazo J.
Nucleic Acids Res. 2015 Apr 16. pii: gkv349.

DeNovoGear 1.1.1 – Detect denovo Mutations using Sequencing data of Related Individuals

DeNovoGear 1.1.1

:: DESCRIPTION

DeNovoGear is a program to detect denovo mutations using sequencing data.

::DEVELOPER

The Cartwright Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Perl
  • C Compiler

:: DOWNLOAD

 DeNovoGear

:: MORE INFORMATION

Citation

Donald F Conrad et al.
Variation in genome-wide mutation rates within and between human families
Nature Genetics 43, 712–714 (2011) doi:10.1038/ng.862

CorMut 1.28.0 – Detect the Correlated Mutations based on Selection Pressure

CorMut 1.28.0

:: DESCRIPTION

CorMut is an R package designed to compute correlated mutations in the unit of codon or amino acid mutation.

::DEVELOPER

CorMut team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 CorMut

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 10. [Epub ahead of print]
CorMut: an R/Bioconductor package for computing correlated mutations based on selection pressure.
Li Z1, Huang Y, Ouyang Y, Jiao Y, Xing H, Liao L, Jiang S, Shao Y, Ma L.

RNASeqMut 0.7 – RNA-Seq Mutation Detection

RNASeqMut 0.7

:: DESCRIPTION

RNASeqMut is an easy-to-use program to detection variants in RNA-Seq read alignments. rnaseqmut is a light-weight C++ program to detect variants (or mutations, including SNPs, indels, RNA editing events) from a single or multiple RNA-Seq BAM files.

::DEVELOPER

Wei Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 RNASeqMut

:: MORE INFORMATION

mirTrios – Detection of de novo and rare inherited Mutations from Trios-based NGS

mirTrios

:: DESCRIPTION

mirTrios was developed for identification and comprehensive analysis the de novo and rare inherited variants with one or multiple trios samples based on high-throughput sequencing data starting from a VCF file (version 4). It uses reference gene definitions and hg19 genomic coordinates for annotation.

::DEVELOPER

mirTrios team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 N/A

:: MORE INFORMATION

Citation

mirTrios: an integrated pipeline for detection of de novo and rare inherited mutations from trios-based next-generation sequencing.
Li J, Jiang Y, Wang T, Chen H, Xie Q, Shao Q, Ran X, Xia K, Sun ZS, Wu J.
J Med Genet. 2015 Apr;52(4):275-81. doi: 10.1136/jmedgenet-2014-102656.

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.

iPAC 1.37.0 – Identification of Protein Amino acid mutation Clustering

iPAC 1.37.0

:: DESCRIPTION

iPAC finds mutation clusters on the amino acid level while taking into account the protein structure.

::DEVELOPER

Zhao Hongyu’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 iPAC

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Jun 13;14:190. doi: 10.1186/1471-2105-14-190.
Utilizing protein structure to identify non-random somatic mutations.
Ryslik GA, Cheng Y, Cheung KH, Modis Y, Zhao H.

iStable – Integrated Predictor for Protein Stability change upon Single Mutation

iStable

:: DESCRIPTION

iStable ,an integrated predictor, constructed by using sequence information and prediction results from different element predictors.

::DEVELOPER

Natural Computing and Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 2:S5. doi: 10.1186/1471-2105-14-S2-S5. Epub 2013 Jan 21.
iStable: off-the-shelf predictor integration for predicting protein stability changes.
Chen CW, Lin J, Chu YW.

MuCor – Mutation Aggregation and Correlation

MuCor

:: DESCRIPTION

MuCor is software to aggregate variant information sourced from multiple VCF files (and some others, see below) into a variety of summary files with varying levels of detail and statistics.

::DEVELOPER

blachly lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Python

:: DOWNLOAD

  MuCor

:: MORE INFORMATION

Citation:

MuCor: Mutation Aggregation and Correlation.
Kroll KW, Eisfeld AK, Lozanski G, Bloomfield CD, Byrd JC, Blachly JS.
Bioinformatics. 2016 Jan 23. pii: btw028