Tag: Regulatory Element

Predector 1.2.3.0 – Dertermine Regulatory Elements in Bacterial Genomes

Predector 1.2.3.0

:: DESCRIPTION

PreDetector (Prokaryotic Regulatory Elements Detector) is a tool designed for biologists. Its main function is to search for the cis-elements (nucleotides) that regulate the genes for a bacteria specie, assuming that one usually consider that a cis sequence regulates a gene iff it is oriented in the same direction and if it is localised in a user-specified interval regarding to the beginning of the gene. To achieve its function, PreDetector connects to the NCBI server, which provides the information on the genes for a given bacteria. When a cis sequence is considerated as regulating a gene, PreDetector also computes the co-transcribed genes, that is the genes that are located in another user-specified interval regarding to the end of the preceding gene (and this is a recursive process). On user demand, PreDetector also allows to generate statistics containing the percentage of genic and intergenic sequences

::DEVELOPER

Samuel Hiard

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 Predector

:: MORE INFORMATION

Citation

Hiard S, Maree R, Colson S, Hoskisson PA, Titgemeyer F, van Wezel GP, Joris B, Wehenkel L, Rigali S. (2007).
PREDetector: A new tool to identify regulatory elements in bacterial genomes.
Biochem Biophys Res Commun. 357(4):861-4.

ReMap 2020 – ChIP-seq analysis of Regulatory Elements

ReMap 2020

:: DESCRIPTION

ReMap is an integrative analysis of transcription factor ChIP-seq experiments

::DEVELOPER

The TAGC Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Cheneby J., Menetrier Z., Mestdagh M., Rosnet T., Douida A., Rhalloussi W., Bergon A., Lopez F., Ballester B.
ReMap 2020: A database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments.
Nucleic Acids Research (2020) gkz945 https://doi.org/10.1093/nar/gkz945.

Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape.
Griffon A, Barbier Q, Dalino J, van Helden J, Spicuglia S, Ballester B.
Nucleic Acids Res. 2015 Feb 27;43(4):e27. doi: 10.1093/nar/gku1280.

RCADE 1.0 – Recognition Code-Assisted Discovery of Regulatory Elements

RCADE 1.0

:: DESCRIPTION

RCADE combines predictions from a DNA recognition code of C2H2-ZFs with ChIP-seq data to identify models that represent the genuine DNA binding prefer-ences of C2H2-ZF proteins.

::DEVELOPER

Hamed S. Najafabadi at the Hughes lab in the Terrence Donnelly Centre for Cellular and Biomolecular Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 RCADE

:: MORE INFORMATION

Citation

Identification of C2H2-ZF binding preferences from ChIP-seq data using RCADE.
Najafabadi HS, Albu M, Hughes TR.
Bioinformatics. 2015 May 6. pii: btv284

regshape v1.1 – DNA Shape-based Classifier for Regulatory Elements(R pkg)

regshape v1.1

:: DESCRIPTION

The regshape R package  provides a classifier for predicting whether a given oligonucleotide sequence (of length l bp, where l would typically vary from six to as high as 25 bp) is, or is not, a transcription factor (TF) binding site.

::DEVELOPER

The Ramsey Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

 regshape

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Jun 30. pii: btv391
A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites.
Yang J, Ramsey SA.

MatrixCatch 2.7 – Recognition of Composite Regulatory Elements in Promoters

MatrixCatch 2.7

:: DESCRIPTION

MatrixCatch (MCatch) is a tool designed to search for potential composite elements (CEs) in DNA sequences.

::DEVELOPER

MatrixCatch team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Aug 8;14:241. doi: 10.1186/1471-2105-14-241.
MatrixCatch–a novel tool for the recognition of composite regulatory elements in promoters.
Deyneko IV, Kel AE, Kel-Margoulis OV, Deineko EV, Wingender E, Weiss S.

CLARE – Cracking the LAnguage of Regulatory Elements

CLARE

:: DESCRIPTION

CLARE is a computational method designed to reveal sequence encryption of tissue-specific regulatory elements.

::DEVELOPER

Ivan Ovcharenko Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Feb 15;28(4):581-3. doi: 10.1093/bioinformatics/btr704. Epub 2011 Dec 22.
CLARE: Cracking the LAnguage of Regulatory Elements.
Taher L1, Narlikar L, Ovcharenko I.

SSpred – Splice Site Prediction with Regulatory Elements and Dependencies

SSpred

:: DESCRIPTION

SSPred is a splice site prediction toolchain which incorporated a statistical model of splicing signals built based on the entropy density profile (EDP) method, weight array method (WAM), and kappa test, and a model of splicing regulatory elements developed by an unsupervised self-learning method to detect motifs associated with splicing regulatory elements.

::DEVELOPER

ZhuLab, Peking Uiniversity, Beijing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 SSPred

:: MORE INFORMATION

PHIRE 1.00 – Reveal Regulatory Elements in Bacteriophage Genomes

PHIRE 1.00

:: DESCRIPTION

PHIRE (PHage In silico Regulatory Elements) is a standalone program in Visual Basic, performs an algorithmic string-based search on bacteriophage genome sequences, discovering and extracting blocks displaying sequence similarity, corresponding to conserved regulatory elements contained within these genomes in a systematic manner, without any prior experimental or predictive knowledge.

::DEVELOPER

Lighthouse data

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

PHIRE

:: MORE INFORMATION

Citation

Lavigne, R., Sun, W.D. and Volckaert, G.
PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes.
Bioinformatics (2004) 20: 629-635.