RED 0.0.3 – RNA Editing sites Detector

RED 0.0.3

:: DESCRIPTION

RED is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data.

::DEVELOPER

RED team

:: SCREENSHOTS

RED

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • JRE

:: DOWNLOAD

 RED

:: MORE INFORMATION

Citation

RED: A Java-MySQL Software for Identifying and Visualizing RNA Editing Sites Using Rule-Based and Statistical Filters.
Sun Y, Li X, Wu D, Pan Q, Ji Y, Ren H, Ding K.
PLoS One. 2016 Mar 1;11(3):e0150465. doi: 10.1371/journal.pone.0150465.

REMOCOD – REgulatory MOtif COmbination Detector

REMOCOD

:: DESCRIPTION

REMOCOD  is a program for the systematic identification of pairs of transcription factor binding sites (TFBSs) that tend to co-occur in promoter sequences of a set of co-regulated genes. Given a set of gene IDs, the program first detects over-represented TFBSs in the promoter sequences corresponding to these genes, and subsequently predicts regulatory motifs that show a tendency to co-occur with any of the over-represented TFBSs.

::DEVELOPER

Systems Immunology Laboratory , Osaka University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Vandenbon A, Kumagai Y, Akira S, Standley DM.
A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription“,
BMC Genomics. 2012;13 Suppl 7:S11. doi: 10.1186/1471-2164-13-S7-S11

FreeBayes 1.3.1 – Bayesian Genetic Variant Detector

FreeBayes 1.3.1

:: DESCRIPTION

FreeBayes is a high-performance, flexible, and open-source Bayesian genetic variant detector. It operates on BAM alignment files, which are produced by most contemporary short-read aligners.

::DEVELOPER

The MarthLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  FreeBayes

:: MORE INFORMATION

Citation

Haplotype-based variant detection from short-read sequencing
Erik Garrison, Gabor Marth

AffyMAPSDetector 1.0 – Affymetrix MicroArray Probe SNP Detector

AffyMAPSDetector 1.0

:: DESCRIPTION

 AffyMAPSDetector stands for Affymetrix MicroArray Probe SNP Detector. It detects the presence of SNPs (Single Nucleotide Polymorphism) in the probes of Affymetrix GeneChipTM expression arrays. However, it can be used to characterize any GeneChipTM with respect to SNPs for which NCBI fully supports gene and SNP annotations (i.e. the organism for which GeneChipTM is desinged and that organism’s genome exists in NCBI nucleotide and SNP database).

DEVELOPER

AffyMAPSDetector Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 AffyMAPSDetector

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Jul 30;8:276.
AffyMAPSDetector: a software tool to characterize Affymetrix GeneChip expression arrays with respect to SNPs.
Kumari S, Verma LK, Weller JW.

Swelfe – Detector of Internal Repeats in Sequences and Structures

Swelfe

:: DESCRIPTION

Swelfe is a program that enables you to find internal repeats in DNA sequences, amino-acid sequences or 3D structures.

::DEVELOPER

 RPBS(Ressource Parisienne en BioInformatique Structurale)

:: SCREENSHOTS

N/A

: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

  Swelfe

:: MORE INFORMATION

Citation:

Anne-Laure Abraham; Eduardo P. C. Rocha; Joel Pothier
Swelfe : a detector of internal repeats in sequences and structures
Bioinformatics 2008; doi: 10.1093/bioinformatics/btn234