Tag: Detect

MendelSoft 0.9.8 – Detect Marker Genotyping Incompatibilities

MendelSoft 0.9.8

:: DESCRIPTION

MendelSoft is an open source software which detects marker genotyping incompatibilities (Mendelian errors only) in complex pedigrees using weighted constraint satisfaction techniques. The input of the software is a pedigree data with genotyping data at a single locus. The output of the software is a list of individuals for which the removal of their genotyping data restores consistency. This list is of minimum size when the program ends.

::DEVELOPER

Simon De Givry, BIA, INRA, Toulouse, France @ The Division of Applied Mathematics and Informatics(MIA)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • C++ Compiler

:: DOWNLOAD

 MendelSoft

:: MORE INFORMATION

Citation

M. Sanchez, S. de Givry, and T. Schiex
Mendelian error detection in complex pedigrees using weighted constraint satisfaction techniques
In Constraints journal, special issue on bioinformatics, 13(1), 2008.

REPPER – Detect Regions with Short Gapless REPeats in Protein Sequences

REPPER

:: DESCRIPTION

REPPER (REPeats and their PERiodicities) is an integrated server that detects and analyzes regions with short gapless repeats in protein sequences or alignments. It finds periodicities by Fourier Transform (FTwin) and internal similarity analysis (REPwin). FTwin assigns numerical values to amino acids that reflect certain properties, for instance hydrophobicity, and gives information on corresponding periodicities. REPwin uses self-alignments and displays repeats that reveal significant internal similarities. Both programs use a sliding window to ensure that different periodic regions within the same protein are detected independently. FTwin and REPwin are complemented by secondary structure prediction (PSIPRED) and coiled coil prediction (COILS), making the server a versatile analysis tool for sequences of fibrous proteins.

::DEVELOPER

Söding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation:

M.Gruber, J. Söding , and A.N.Lupas (2005)
REPPER – repeats and their periodicities in fibrous proteins
Nucl. Acids Res., 33(2), W239-43

ASC 0.1.4 – Empirical Bayes method to detect Differential Expression

ASC 0.1.4

:: DESCRIPTION

ASC (Analysis of Sequence Counts) borrows information across sequences to establish prior distribution of sample variation, so that biological variation can be accounted for even when replicates are not available. Compared current approaches that simply tests for equality of proportions in two samples, ASC is less biased towards highly expressed sequences and can identify more genes with a greater log fold change at lower overall abundance.

::DEVELOPER

Zhijin Wu PhD

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package

:: DOWNLOAD

 ASC

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Nov 16;11:564. doi: 10.1186/1471-2105-11-564.
Empirical bayes analysis of sequencing-based transcriptional profiling without replicates.
Wu Z, Jenkins BD, Rynearson TA, Dyhrman ST, Saito MA, Mercier M, Whitney LP.

Immanc 5.0 – Detecting Immigrants Using Multilocus Genotypes

Immanc 5.0

:: DESCRIPTION

immanc is a program designed to test whether or not an individual is an immigrant or is of recent immigrant ancestry.

::DEVELOPER

Rannala Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/ WIndows

:: DOWNLOAD

 Immanc

:: MORE INFORMATION

Citation

Rannala, B., and J. L. Mountain. 1997.
Detecting immigration by using multilocus genotypes.
Proceedings of the National Academy of Sciences USA 94: 9197-9201.

MCMC_IBDfinder 1.0 – Detect IBD Regions simultaneously in Multiple Individuals

MCMC_IBDfinder 1.0

:: DESCRIPTION

MCMC_IBDfinder is a c++ program that estimates posterior probabilities of identity by descent (IBD) sharing between multiple individuals using unphased single nucleotide polymorphism (SNP) data.

::DEVELOPER

Ida Moltke

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Mac OsX
  • C++ Compiler

:: DOWNLOAD

 MCMC_IBDfinder

:: MORE INFORMATION

Citation

A method for detecting IBD regions simultaneously in multiple individuals — with applications to disease genetics
Ida Moltke, Anders Albrechtsen, Thomas v. O. Hansen, Finn C Nielsen and Rasmus Nielsen
Genome Res. 2011 Jul;21(7):1168-80.

ADAPTSITE 1.6 – Detect Natural Selection at Single Amino Acid Sites

ADAPTSITE 1.6

:: DESCRIPTION

ADAPTSITE is a method of detecting positive and negative selection at single codon sites.

::DEVELOPER

Yoshiyuki Suzuki

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOSX
  • C Compiler

:: DOWNLOAD

 ADAPTSITE

:: MORE INFORMATION

Citation:

Suzuki Y. and Gojobori T. (1999)
A method for detecting positive selection at single amino acid sites.
Mol. Biol. Evol. 16:1315-1328.

PERM 1.0 – Detect Structuring Factors in meaningful Social Units

PERM 1.0

:: DESCRIPTION

PERM is a permutation program designed to detect statistical connections between grouping structures and grouping factors or correlates. PERM offers four procedures: i) Detecting a statistical link between a collection of groups and some pairwise relationship statistic such as Rxy, Mxy, half or fullsibship; ii) Comparing average values among groups for some measure or statistic; iii) Searching for connections between group structure and category e.g. population membership; iv) Detecting a statistical connection between mating couple formation and some pairwise relationship between partners such as allelic distance on an MHC locus.

:: DEVELOPER

Dr Louis Bernatchez

:: SCREENSHOTS

perm

:: REQUIREMENTS

  • Windows / MacOsX
  • Excel

:: DOWNLOAD

 PERM

:: MORE INFORMATION

Citation

DUCHESNE, P., C. éTIENNE, L. BERNATCHEZ. 2006.
PERM: A computer program to detect structuring factors in meaningful social units.
Molecular Ecology Notes. 6: 965-976.

MutSig Beta – Detect Significantly Mutated Genes

MutSig Beta

:: DESCRIPTION

MutSig (for “Mutation Significance”) is a package of tools for analyzing mutation data.  It operates on a cohort of patients and identifies mutations, genes, and other genomic elements predicted to be driver candidates.  MutSig was developed for the use case of somatic mutations, i.e. mutations that occurred during the development of cancer, and this documentation uses language specific to somatic mutations.  However, MutSig has also been used for analysis of germline mutations and is completely applicable to that use case also.

::DEVELOPER

The Cancer Genome Analysis (CGA) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MutSig

:: MORE INFORMATION

Citation

Shantanu Banerji,et al.
Sequence analysis of mutations and translocations across breast cancer subtypes
Nature 486, 405–409 (21 June 2012) doi:10.1038/nature11154

3SEQ 1.1.0812 – Software for Detecting Recombination in Sequence data

3SEQ 1.1.0812

:: DESCRIPTION

3SEQ is a software program for identifying mosaic structure or recombination in nucleotide sequence data. 3SEQ takes as input a data set with a minimum of three aligned sequences, and it tests whether any sequence in the data set is a recombinant or mosaic of any other two sequences in the data set.

::DEVELOPER

the Mathematical Modeling and Bioinformatics Group at the Oxford University Clinical Research Unit (OUCRU)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • C++ Compiler

:: DOWNLOAD

  3SEQ 

:: MORE INFORMATION

Citation

Boni MF, Posada D, Feldman MW.
An exact nonparametric method for inferring mosaic structure in sequence triplets.
Genetics, 176:1035-1047, 2007.

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