Tag: Mutation

MMAPPR 0.83 – Mutation Mapping Analysis Pipeline for Pooled RNA-seq

MMAPPR 0.83

:: DESCRIPTION

MMAPPR is an analysis pipeline for mapping mutations using RNA-seq. It works without parental strain information, without the requirement of a pre-existing snp map of the organism, and without erroneous assumptions that recombination occurs at the same frequency across the genome.

::DEVELOPER

Yost Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • Python
  • R package

:: DOWNLOAD

 MMAPPR

:: MORE INFORMATION

Citation

Hill, J. T., Demarest, B. L., Bisgrove, B. W., Gorsi, B., Su, Y.-C., & Yost, H. J. (2013).
MMAPPR: Mutation Mapping Analysis Pipeline for Pooled RNA-seq.
Genome Res. 2013 Apr;23(4):687-97.

I-Mutant 2.0.7 – A Tool for Predicting Protein Stability upon Mutation

I-Mutant 2.0.7

:: DESCRIPTION

I-Mutant is a support vector machine (SVM)-based tool for the automatic prediction of protein stability changes upon single point mutations. The software’s predictions are performed starting either from the protein structure or, more importantly, from the protein sequence.

::DEVELOPER

the Structural Bioinformatics Unit

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Python

:: DOWNLOAD

 I-Mutant

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W306-10.
I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure.
Capriotti E, Fariselli P, Casadio R.

CHuM – Cis-acting Human Mutation

CHuM

:: DESCRIPTION

CHuM is a computational discrimination strategy for regulatory polymorphisms in the upstream non-coding regions.

::DEVELOPER

 the laboratory of Stephen B. Montgomery

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Perl

:: DOWNLOAD

  CHuM

:: MORE INFORMATION

Citation

Montgomery S.B., Griffith O.L., Schuetz J.M., Brooks-Wilson, A., Jones S.J.M.
“A Computational Discrimination Strategy For Regulatory Polymorphisms In The Upstream Non-Coding Regions of Homo Sapiens”
(Submitted).

 

SNAP – Predicts Effect of Mutations on Protein Function

SNAP

:: DESCRIPTION

SNAP (screening for non-acceptable polymorphisms) is a method for evaluating effects of single amino acid substitutions on protein function.SNAP identifies over 80% of the non-neutral mutations at 77% accuracy and over 76% of the neutral mutations at 80% accuracy at its default threshold. Each prediction is associated with a reliability index that correlates with accuracy and thereby enables experimentalists to zoom into the most promising predictions.

::DEVELOPER

Yana Bromberg in Rost Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 available upon request.

:: MORE INFORMATION

Citation

SNAP predicts effect of mutations on protein function.
Bromberg Y, Yachdav G, Rost B.
Bioinformatics. 2008 Oct 15;24(20):2397-8. Epub 2008 Aug 30.

MitoDis – Detection of Mitochondrial DNA mutation Involvement in Diseases

MitoDis

:: DESCRIPTION

MitoDis is intended to implement a test to detect mitochondrial DNA mutation involvement.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 MitoDis

:: MORE INFORMATION

Citation

Sun FZ, Cui J, Gavras H, and Schwartz F.
A Novel Class of Tests for the Detection of Mitochondrial DNA Mutation Involvement in Diseases.
Am. J. Hum. Genet. 72 (2003) pp. 1515-1526

EffiSim – Measuring Efficiency of Mutations Screens for Recessive Phenotypes

EffiSim

:: DESCRIPTION

EffiSim is a script that calculates two measures of the efficiency of a genome- wide mutation screen for recessive phenotypes and performs simulations to confirm results

EffiSim Onilne Version

::DEVELOPER

WEHI Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 EffiSim

:: MORE INFORMATION

Citation:

Silver J.D, Hilton D.J., Bahlo M., Kile B.T. (2006)
Efficient breeding strategies for the generation of ENU mutant mice with recessive phenotypes.

SIBMED 1.0 – Identify Likely Genotyping Errors and Mutations

SIBMED 1.0

:: DESCRIPTION

SIBMED ((SIBpair Mutation and Error Detection)) is a FORTRAN 77 program that identifies likely genotyping errors and mutations for a sib pair in the context of multipoint mapping.Specifically, using a hidden Markov model, the program calculates the posterior probability of genotyping error or mutation for each sib-pair-marker combination, given all the available marker data, an assumed genotype-error rate, and a known genetic map.  The subset of combinations for which this posterior error probability is high may be considered for exclusion, review, or retyping.

::DEVELOPER

the Center for Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • FORTRAN

:: DOWNLOAD

  SIBMED

:: MORE INFORMATION

Citation

Douglas JA, Boehnke M, Lange K (2000)
A multipoint method for detecting genotyping errors and mutations in sibling-pair linkage data.
Am J Hum Genet 66: 1287-1297