HCMV / MRA – Drug / Mutation Resistance Mutations

HCMV / MRA

:: DESCRIPTION

HCMV (human cytomegalovirus) is a new tool linking human cytomegalovirus drug resistance mutations to resistance phenotypes.

MRA is a new tool linking drug resistance mutations to resistance phenotypes.

::DEVELOPER

Medical Systems Biology, University of Ulm

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Antiviral Res. 2010 Feb;85(2):318-27. doi: 10.1016/j.antiviral.2009.10.004. Epub 2009 Oct 22.
A new tool linking human cytomegalovirus drug resistance mutations to resistance phenotypes.
Chevillotte M1, von Einem J, Meier BM, Lin FM, Kestler HA, Mertens T.

Rediscover 0.3.0 – Identify Mutually Exclusive Mutations

Rediscover 0.3.0

:: DESCRIPTION

Rediscover is an optimized method for identifying mutually exclusive genomic events.

::DEVELOPER

Juan A. Ferrer-Bonsoms Developer <jafhernandez at tecnun.es>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • R

:: DOWNLOAD

Rediscover

:: MORE INFORMATION

Citation

Ferrer-Bonsoms JA, Jareno L, Rubio A.
Rediscover: an R package to identify mutually exclusive mutations.
Bioinformatics. 2021 Oct 19:btab709. doi: 10.1093/bioinformatics/btab709. Epub ahead of print. PMID: 34664620.

Gene Machine 1.04 – Simulation of Mutations within the Lac Operon

Gene Machine 1.04

:: DESCRIPTION

Gene Machine builds a gene network! The lac operon is a set of genes which are responsible for the metabolism of lactose in some bacterial cells. Explore the effects of mutations within the lac operon by adding or removing genes from the DNA.

::DEVELOPER

the PhET™ project at the University of Colorado

:: SCREENSHOTS

GeneMachine

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • Java

:: DOWNLOAD

 Gene Machine

:: MORE INFORMATION

Citation

Science. 2008 Oct 31;322(5902):682-3. doi: 10.1126/science.1161948.
PHYSICS. PhET: simulations that enhance learning.
Wieman CE, Adams WK, Perkins KK.

HotMAPS v1.1.4 – Hotspot Missense mutation Areas in Protein Structures

HotMAPS v1.1.4

:: DESCRIPTION

HotMAPS detects somatic mutation hotspot regions in 3D protein structures.

::DEVELOPER

Karchin Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

HotMAPS

:: MORE INFORMATION

Citation

Tokheim C, Bhattacharya R, Niknafs N, Gygax DM, Kim R, Ryan M, Masica DL, Karchin R.
Exome-Scale Discovery of Hotspot Mutation Regions in Human Cancer Using 3D Protein Structure.
Cancer Res. 2016 Jul 1;76(13):3719-31. doi: 10.1158/0008-5472.CAN-15-3190. Epub 2016 Apr 28. PMID: 27197156; PMCID: PMC4930736.

AlloSigMA 2 – Allosteric Signalling and Mutation Analysis

AlloSigMA 2

:: DESCRIPTION

The AlloSigMA server is a tool for estimating the allosteric free energies acting on a single residue as a result of either ligand binding, mutations, or both combined.

::DEVELOPER

Bioinformatics Institute (BII), Singapore.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Tan ZW, Guarnera E, Tee WV, Berezovsky IN.
AlloSigMA 2: paving the way to designing allosteric effectors and to exploring allosteric effects of mutations.
Nucleic Acids Res. 2020 Jul 2;48(W1):W116-W124. doi: 10.1093/nar/gkaa338. PMID: 32392302; PMCID: PMC7319554.

HPMV – Human (Protein) Mutation Viewer

HPMV

:: DESCRIPTION

HPMV: Human (Protein)  Mutation Viewer

::DEVELOPER

the Bioinformatics Institute (BII), Singapore.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • Java

:: DOWNLOAD

 HPMV

:: MORE INFORMATION

Citation

Sherman WA, Kuchibhatla DB, Limviphuvadh V, Maurer-Stroh S, Eisenhaber B, Eisenhaber F.
HPMV: human protein mutation viewer – relating sequence mutations to protein sequence architecture and function changes.
J Bioinform Comput Biol. 2015 Oct;13(5):1550028. doi: 10.1142/S0219720015500286. Epub 2015 Oct 27. PMID: 26503432.

DESnowball 1.0 – Method to Identify Downstream Target Genes that are affected by a recurrent driver Mutation

DESnowball 1.0

:: DESCRIPTION

DESnowball R package implements the snowball approach, a highly sensitive statistical analysis method to identify downstream target genes that are affected by a recurrent driver mutation.

::DEVELOPER

Bioinformatics and Systems Medicine Laboratory

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux  / WIndows / MacOsX
  • R

:: DOWNLOAD

 DESnowball

:: MORE INFORMATION

Citation:

Snowball: resampling combined with distance-based regression to discover transcriptional consequences of a driver mutation.
Xu Y, Guo X, Sun J, Zhao Z.
Bioinformatics. 2014 Sep 5. pii: btu603

MutationTaster 2021 – Mutation Prediction for the Deep-sequencing Age

MutationTaster 2021

:: DESCRIPTION

MutationTaster is a free web-based application to evaluate DNA sequence variants for their disease-causing potential. The software performs a battery of in silico tests to estimate the impact of the variant on the gene product / protein.

::DEVELOPER

MutationTaster team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Steinhaus R, Proft S, Schuelke M, Cooper DN, Schwarz JM, Seelow D.
MutationTaster2021.
Nucleic Acids Res. 2021 Jul 2;49(W1):W446-W451. doi: 10.1093/nar/gkab266. PMID: 33893808; PMCID: PMC8262698.

Schwarz JM, Cooper DN, Schuelke M, Seelow D.
MutationTaster2: mutation prediction for the deep-sequencing age.
Nat Methods. 2014 Apr;11(4):361-2. doi: 10.1038/nmeth.2890. PMID: 24681721.

SCmut – Detect Cell-level Mutation from single-cell RNA-sequencing

SCmut

:: DESCRIPTION

SCmut is a novel and robust statistical method for cell-level somatic mutation detection from single-cell RNA-sequencing.

::DEVELOPER

PROF. YUDI PAWITAN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

SCmut

:: MORE INFORMATION

Citation

Vu TN, Nguyen HN, Calza S, Kalari KR, Wang L, Pawitan Y.
Cell-level somatic mutation detection from single-cell RNA sequencing.
Bioinformatics. 2019 Nov 1;35(22):4679-4687. doi: 10.1093/bioinformatics/btz288. PMID: 31028395; PMCID: PMC6853710.

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