TrackSig – Reconstructing Evolutionary Trajectories of Mutations in Cancer

TrackSig

:: 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

Morris Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
  • Python

:: DOWNLOAD

TrackSig

:: 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

Cancer3D 2.0 – Patterns of Mutations in Cancer

Cancer3D 2.0

:: 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

Godzik Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser
:: DOWNLOAD

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.

CCMpred 0.3.2 – Prediction of Protein Residue-residue Contacts from Correlated Mutations

CCMpred 0.3.2

:: DESCRIPTION

CCMpred is a C implementation of a Markov Random Field pseudo-likelihood maximization for learning protein residue-residue contacts

::DEVELOPER

Söding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler
:: DOWNLOAD

 CCMpred

:: 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

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

MAPOR 1.0 – MutAtion LandscaPe GeneratOR

MAPOR 1.0

:: DESCRIPTION

MAPOR is a program for analyzing the mutational landscape of proteins. It uses an energy function that computes the Lennard-Jones, Coulomb, and solvation energies to determine the effect of a mutation on a protein’s stability.

::DEVELOPER

MAPOR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 MAPOR

:: MORE INFORMATION

SEMBA – Single-rEsidue Mutational based Binding Affinity

SEMBA

:: DESCRIPTION

SEMBA is a program for analyzing the binding affinity of amyloid proteins. It uses an energy function that computes the Lennard-Jones, Coulomb, and solvation energies
to determine the effect of a mutation on a protein’s stability.

::DEVELOPER

SEMBA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 SEMBA

:: MORE INFORMATION

Citation

Probing the binding affinity of amyloids to reduce toxicity of oligomers in diabetes.
Smaoui MR, Orland H, Waldispühl J.
Bioinformatics. 2015 Mar 15. pii: btv143.

RNAmutants 2.0 – Analysis of RNA Mutational Landscapes

RNAmutants 2.0

:: 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

  • Linux /  Mac OsX

:: DOWNLOAD

 RNAmutants 

:: 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.

RNAMute / XRNAmute – RNA Secondary Structure Mutation Analysis Tool

RNAMute / XRNAmute

:: 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

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

 RNAMute

:: 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.

DUET – Predicting Effects of Mutations on Protein Stability

DUET

:: DESCRIPTION

DUET is a web server for an integrated computational approach for studying missense mutations in proteins.

::DEVELOPER

Dr. Douglas E. V. Pires

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach.
Pires DE, Ascher DB, Blundell TL.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W314-9. doi: 10.1093/nar/gku411.

MCV – Mutation Calling with VAF for Whole Genome Sequencing

MCV

:: 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

  • Linux

:: DOWNLOAD

 MCV

:: MORE INFORMATION