Tag: Hotspot

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.

HotSpot – Hot Spot Residues Prediction

HotSpot

:: DESCRIPTION

Hot Spot is a software of prediction of hot spot residues through physicochemical characteristics of amino acid sequences

::DEVELOPER

Structural and Functional Bioinformatics Group, King Abdullah University of Science and Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  HotSpot

:: MORE INFORMATION

Citation

Proteins. 2013 Aug;81(8):1351-62. doi: 10.1002/prot.24278.
Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences.
Chen P1, Li J, Wong L, Kuwahara H, Huang JZ, Gao X.

HotspotFisher – Detect Recombination Hotspots from Population Polymorphism data

HotspotFisher

:: DESCRIPTION

HotspotFisher is a package for detecting recombination hotspots from population polymorphism data. HotspotFisher uses a multi-hotspot model and the truncated weighted pairwise log-likelihood (TWPLL), so it can detect multiple hotspots in a region. HotspotFisher can be used to both phased/haplotype and unphased/genotype data directly, with arbitrary levels of missing data.

::DEVELOPER

Jun Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows

:: DOWNLOAD

 HotspotFisher

:: MORE INFORMATION

Citation

Jun Li, Michael Q Zhang, Xuegong Zhang (2006)
A New Method for Detecting Human Recombination Hotspots and Its Applications to the HapMap ENCODE Data.
The American Journal of Human Genetics 79:628-639.

iRSpot-Pse6NC 2.0 – Identifying Recombination Hotspots in Saccharomyces Cerevisiae

iRSpot-Pse6NC 2.0

:: DESCRIPTION

Based on dataset containing both ORF and non-ORF recombination sites, iRSpot-Pse6NC is a predictor which using SVM classifier by incorporating the key hexamer features into the general PseKNC (Pseudo K-tuple Nucleotide Composition) via the binomial distribution feature selection approach.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

A comparison and assessment of computational method for identifying recombination hotspots in Saccharomyces cerevisiae.
Yang H, Yang W, Dao FY, Lv H, Ding H, Chen W, Lin H.
Brief Bioinform. 2019 Oct 21. pii: bbz123. doi: 10.1093/bib/bbz123

iRSpot-Pse6NC: Identifying recombination spots in Saccharomyces cerevisiae by incorporating hexamer composition into general PseKNC.
Int J Biol Sci. 2018 May 22;14(8):883-891. doi: 10.7150/ijbs.24616. eCollection 2018.
Yang H, Qiu WR, Liu G, Guo FB, Chen W, Chou KC, Lin H.

HotSpot3D 1.8.0 – 3D Hotspot Mutation Proximity Analysis tool

HotSpot3D 1.8.0

:: DESCRIPTION

HotSpot3D can be used to identify the mutation hotspots in the linear 1D sequence and correlates these hotspots with known or potential interacting domains based on both known intermolecular interactions and calculated proximity for potential intramolecular interactions.

::DEVELOPER

Ding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HotSpot3D

:: MORE INFORMATION

Citation

Nat Genet. 2016 Aug;48(8):827-37. doi: 10.1038/ng.3586. Epub 2016 Jun 13.
Protein-structure-guided discovery of functional mutations across 19 cancer types.
Niu B, Scott AD, Sengupta S, Bailey MH, Batra P, Ning J, Wyczalkowski MA, Liang WW, Zhang Q, McLellan MD, Sun SQ, Tripathi P, Lou C, Ye K, Mashl RJ, Wallis J, Wendl MC, Chen F, Ding L

SNPsim 0.8 – Coalescent Simulation of Hotspot Recombination

SNPsim 0.8

:: DESCRIPTION

SNPsim is a population genetic simulator that generates samples of SNP (Single Nucleotide Polymorphisms) haplotypes and diploid biallelic genotypes.

::DEVELOPER

Phylogenomics Group @ the University of Vigo, Spain

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 SNPsim

:: MORE INFORMATION

Citation

Posada D and Wiuf C. 2003.
Simulating haplotype blocks in the human genome.
Bioinformatics 19: 289-290.

msHOT 20080815 – modifying ms that allows Hotspots of Recombination and Gene Conversion

msHOT 20080815

:: DESCRIPTION

msHOT, modifying Hudson’s ms simulator, allows for implementation of multiple crossover hotspots and/or multiple gene conversion hotspots in the simulated genetic region.

::DEVELOPER

Garrett Hellenthal and Matthew Stephens

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 msHOT

:: MORE INFORMATION

Citation:

Hellenthal, G and M. Stephens.
msHOT: modifying Hudson’s ms simulator to incorporate crossover and gene conversion hotspots.
Bioinformatics. 2007 Feb 15;23(4):520-1.

sequenceLDhot – Hotspot Detection

sequenceLDhot

:: DESCRIPTION

sequenceLDhot is further R code for implementing a penalised likelihood approach for detecting hotspots using the output of sequenceLDsr

::DEVELOPER

Prof Paul Fearnhead

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 sequenceLDhot

:: MORE INFORMATION

Citation

Paul Fearnhead, and Nick G.C. Smith
“A novel method with improved power to detect recombination hotspots from polymorphism data reveals multiple hotspots in human genes”
American Journal of Human Genetics, 77 781-794..

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