mmCSM-NA – Predicting Effects of Single and Multiple Mutations on Protein-nucleic Acid Binding affinity

mmCSM-NA

:: DESCRIPTION

mmCSM-NA is the first scalable method capable of quantitatively and accurately predicting the effects of multiple-point mutations on nucleic acid binding affinities.

::DEVELOPER

Biosig Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Nguyen TB, Myung Y, de Sá AGC, Pires DEV, Ascher DB.
mmCSM-NA: accurately predicting effects of single and multiple mutations on protein-nucleic acid binding affinity.
NAR Genom Bioinform. 2021 Nov 17;3(4):lqab109. doi: 10.1093/nargab/lqab109. PMID: 34805992; PMCID: PMC8600011.

PolySearch 2 – Text Mining system for extracting relationships between Human Diseases, Genes, Mutations, Drugs and Metabolites

PolySearch 2

:: DESCRIPTION

PolySearch2 is an online text-mining system for identifying relationships between biomedical entities such as human diseases, genes, SNPs, proteins, drugs, metabolites, toxins, metabolic pathways, organs, tissues, subcellular organelles, positive health effects, negative health effects, drug actions, Gene Ontology terms, MeSH terms, ICD-10 medical codes, biological taxonomies and chemical taxonomies.

::DEVELOPER

the Wishart Research Group, University of Alberta

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more.
Liu Y, Liang Y, Wishart D.
Nucleic Acids Res. 2015 Apr 29. pii: gkv383

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W399-405. doi: 10.1093/nar/gkn296. Epub 2008 May 16.
PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites.
Cheng D, Knox C, Young N, Stothard P, Damaraju S, Wishart DS.

xseq 0.2.1 – Assessing Functional Impact on Gene Expression of Mutations in Cancer

xseq 0.2.1

:: DESCRIPTION

Cancer driver mutations control outcomes indirectly through intermediate phenotypes, e.g., gene expression and protein expression. xseq is a probabilistic model which aims to encode the impact of somatic mutations on gene expression profiles.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
R

:: DOWNLOAD

xseq

:: MORE INFORMATION

Citation

Nat Commun. 2015 Oct 5;6:8554. doi: 10.1038/ncomms9554.
Systematic analysis of somatic mutations impacting gene expression in 12 tumour types.
Ding J et al.

reHCstar 2.1.5 – Algorithm for Haplotype Inference problem on Pedigree data with Recombinations, Errors and Mutations

reHCstar 2.1.5

:: DESCRIPTION

reHCstar is a SAT-based program to compute a haplotype configuration on pedigrees with recombinations, genotyping errors, and missing genotypes.

::DEVELOPER

AlgoLab

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux
CMake
GNU make
Boost FileSystem, System, DateTime, ProgramOptions, IOStreams, and other include-only libraries
Apache Log4cxx

:: DOWNLOAD

reHCstar

:: MORE INFORMATION

Citation

Yuri Pirola, Gianluca Della Vedova, Stefano Biffani, Alessandra Stella, and Paola Bonizzoni.
A fast and practical approach to genotype phasing and imputation on a pedigree with erroneous and incomplete information.
IEEE/ACM Transactions on Computational Biology and Bioinformatics (2012).

QuantumClone 1.0.0.6 – Clustering Mutations using High Throughput Sequencing (HTS) Data

QuantumClone 1.0.0.6

:: DESCRIPTION

QuantumClone is a clonal reconstruction method for whole genome or whole exome sequencing data.

::DEVELOPER

Boeva lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX/ Windows
R

:: DOWNLOAD

QuantumClone

:: MORE INFORMATION

Citation

Deveau P, et al.
QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction.
Bioinformatics. 2018 Jun 1;34(11):1808-1816. doi: 10.1093/bioinformatics/bty016. PMID: 29342233; PMCID: PMC5972665.

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

Biosig Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

WEb browser

:: DOWNLOAD

:: 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.

MIMP – Predicting the Impact of Mutations on Kinase-substrate Phosphorylation

MIMP

:: DESCRIPTION

MIMP characterizes genetic variants such as cancer mutations that specifically alter kinase-binding sites in proteins.

::DEVELOPER

Bader Lab University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser / Linux
R

:: DOWNLOAD

MIMP

:: MORE INFORMATION

Citation

MIMP: predicting the impact of mutations on kinase-substrate phosphorylation.
Wagih O, Reimand J, Bader GD.
Nat Methods. 2015 Jun;12(6):531-3. doi: 10.1038/nmeth.3396.

RNAmapper v1 – Use of RNA-Seq data to Map and Identify Mutations in Zebrafish

RNAmapper v1

:: DESCRIPTION

RNAmapper uses RNA-seq data to identify both a region of the genome linked to a mutation as well as candidate mutations that may be causal for the phenotype of interest. We have shown that the method can identify mutations that cause nonsense or missense changes to codons, alter transcript splicing, or alter gene expression levels. Here you will find information on how to map your mutations using RNA-Seq data.

::DEVELOPER

Adam Miller, Arish Shah, and Cecilia Moens

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / MacOSX /Linux
R package / Galaxy

:: DOWNLOAD

RNAmapper

:: MORE INFORMATION