:: DESCRIPTION
MCV is a pipeline to identify somatic substitutions and indels with VAF (variant allele frequency) from whole genome sequencing
::DEVELOPER
Laboratory for Medical Science Mathematics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
TrackSig is a method to estimate the evolutionary trajectories of signatures of somatic mutational processes. TrackSig uses cancer cell fraction (CCF) corrected by copy number to infer an approximate order in which the somatic mutations accumulate. TrackSig segments mutation ordering by CCF and fits signature exposures (activities) as a piece-wise constant function of the mutation ordering. TrackSig uses optimal segmentation to find the points of change in signature activities.
TrackSigFreq is an R package for TrackSig
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
TrackSig: reconstructing evolutionary trajectories of mutations in cancer
Yulia Rubanova, Ruian Shi, Roujia Li, Jeff Wintersinger, Nil Sahin, Amit Deshwar, Quaid Morris, PCAWG Evolution and Heterogeneity Working Group, PCAWG network
doi: https://doi.org/10.1101/260471
:: DESCRIPTION
Cancer3D database provides an open and user-friendly way to analyze cancer missense mutations in the context of structures of proteins they are found in and in relation to patients gender and age.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
NO
:: MORE INFORMATION
Citation:
Cancer3D 2.0: interactive analysis of 3D patterns of cancer mutations in cancer subsets.
Sedova M, Iyer M, Li Z, Jaroszewski L, Post KW, Hrabe T, Porta-Pardo E, Godzik A.
Nucleic Acids Res. 2019 Jan 8;47(D1):D895-D899. doi: 10.1093/nar/gky1098.
:: DESCRIPTION
CCMpred is a C implementation of a Markov Random Field pseudo-likelihood maximization for learning protein residue-residue contacts
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation:
Bioinformatics. 2014 Jul 26. pii: btu500.
CCMpred-fast and precise prediction of protein residue-residue contacts from correlated mutations.
Seemayer S1, Gruber M1, Söding J
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: DESCRIPTION
RNAmutants is a web server to perform mutational analysis for a given RNA sequence. Previous methods relied on exhaustively enumerating k-point mutant sequences and subsequently applying mfold or RNAfold, a procedure with run time exponential in k. In contrast, RNAmutants computes the minimum free energy structure and Boltzmann partition function for all k-point mutants, for 0 ≤ k ≤ K, with run time O(K2n3).
::DEVELOPER
Clote Lab , Computer Science and Biology at McGill
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
J Comput Biol. 2011 Nov;18(11):1465-79. doi: 10.1089/cmb.2011.0181. Epub 2011 Oct 28.
An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure.
Waldispühl J1, Ponty Y.
Jerome Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote.
Efficient algorithms for probing the RNA mutation landscape.
PLoS Comput Biol. 2008 Aug 8;4(8):e1000124.
:: DESCRIPTION
RNAmute is an application that provides a user friendly interface for analyzing the effects of point mutations on RNAs secondary structure.
XRNAmute is RNAmute web server for the mutational analysis of RNA secondary structures.
::DEVELOPER
A.Churkin and D. Barash (dbarash@cs.bgu.ac.il)
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W92-9. doi: 10.1093/nar/gkr207. Epub 2011 Apr 7.
The RNAmute web server for the mutational analysis of RNA secondary structures.
Churkin A1, Gabdank I, Barash D.
A.Churkin and D. Barash,
“RNAMute: RNA Secondary Structure Mutation Analysis Tool,”
BMC Bioinformatics, 7:221, 2006.
:: DESCRIPTION
The CMAT is a fully automated and reliable web-server for correlated mutation analysis. CMAT automatically performs all the processes for correlated mutation analysis including homology search, multiple sequence alignment construction, sequence redundancy treatment, and various correlated mutation score measures.
:: DEVELOPER
Bioinformatics and Computational Biology Laboratoty,Korea Advanced Institute of Science and Technology (KAIST).
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Protein Eng Des Sel. 2012 Nov;25(11):705-13. doi: 10.1093/protein/gzs081. Epub 2012 Oct 16.
Reliable and robust detection of coevolving protein residues.
Jeong CS, Kim D.
:: DESCRIPTION
CanPredict uses a combination of computational methods to identify those changes most likely to be cancer-associated. Paste your sequence and change(s) below to generate a prediction.
::DEVELOPER
Josh Kaminker (kaminker@gene.com) or Yan Zhang (yz5@gene.com) in Dr. Zemin Zhang’s group in the Bioinformatics department at Genentech.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
CanPredict: a computational tool for predicting cancer-associated missense mutations.
Kaminker JS, Zhang Y, Watanabe C, Zhang Z.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W595-8.
:: DESCRIPTION
MegaMapper is a computational pipeline for positional cloning of mutations by whole genome sequencing.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Development. 2012 Nov;139(22):4280-90. doi: 10.1242/dev.083931. Epub 2012 Oct 10.
Rapid positional cloning of zebrafish mutations by linkage and homozygosity mapping using whole-genome sequencing.
Obholzer N, Swinburne IA, Schwab E, Nechiporuk AV, Nicolson T, Megason SG.
