Tag: Regulatory

PARS – Protein Allosteric and Regulatory Sites

PARS

:: DESCRIPTION

PARS is a server for the prediction of allosteric and regulatory sites on protein structures. PARS queries protein dynamics and structural conservation to identify pockets that may exert a regulatory effect upon binding of a small-molecule ligand.

::DEVELOPER

Xavier Daura

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 May 1;30(9):1314-5. doi: 10.1093/bioinformatics/btu002. Epub 2014 Jan 9.
PARS: a web server for the prediction of Protein Allosteric and Regulatory Sites.
Panjkovich A1, Daura X.

RSAT 2015 – Regulatory Sequence Analysis Tools

RSAT 2015

:: DESCRIPTION

RSAT (Regulatory Sequence Analysis Tools) comprises a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences.

::DEVELOPER

RSAT TEam

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

RSAT 2015: Regulatory Sequence Analysis Tools.
Medina-Rivera A, Defrance M, Sand O, Herrmann C, Castro-Mondragon JA, Delerce J, Jaeger S, Blanchet C, Vincens P, Caron C, Staines DM, Contreras-Moreira B, Artufel M, Charbonnier-Khamvongsa L, Hernandez C, Thieffry D, Thomas-Chollier M, van Helden J.
Nucleic Acids Res. 2015 Apr 22. pii: gkv362.

Thomas-Chollier M, Defrance M, Medina-Rivera A, Sand O, Herrmann C, Thieffry D, van Helden J. (2011)
RSAT 2011: regulatory sequence analysis tools.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W86-91

FunciSNP 1.32.0 – Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs

FunciSNP 1.32.0

:: DESCRIPTION

FunciSNP integrates information from GWAS, 1000genomes and chromatin feature to identify functional SNP in coding or non-coding regions.

::DEVELOPER

FunciSNP  team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 FunciSNP

:: MORE INFORMATION

Citation

FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs.
Coetzee SG, Rhie SK, Berman BP, Coetzee GA, Noushmehr H.
Nucleic Acids Res. 2012 Oct;40(18):e139. doi: 10.1093/nar/gks542.

regEfmtool 3.3 – Regulatory Elementary Flux Mode Tool

regEfmtool 3.3

:: DESCRIPTION

regEfmtool is a computational tool that combines the calculation of elementary flux modes in metabolic networks with transcriptional regulatory networks. regEfmtool is based on the open source software efmtool 

::DEVELOPER

regEfmtool team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 regEfmtool

:: MORE INFORMATION

Citation

regEfmtool: speeding up elementary flux mode calculation using transcriptional regulatory rules in the form of three-state logic.
Jungreuthmayer C, Ruckerbauer DE, Zanghellini J.
Biosystems. 2013 Jul;113(1):37-9. doi: 10.1016/j.biosystems.2013.04.002.

Precise – Predict Regulatory Cis-acting Elements

Precise

:: DESCRIPTION

PRECISE can predict regulatory cis-acting elements through DNA sequences. It aimed at advanced mining of specific biological data: sequence data of DNA sequences that lie upstream of regions with known coding function.

PRECISE performs an extensive (and computation time intensive) search and comparison through these DNA sequences to look for common fragments (motifs, boxes).

PRECISE highlights common fragments and can yield a complete presence/absence table for all found boxes and sequences which an be used for further statistical analysis.

::DEVELOPER

Wageningen UR Plant Breeding

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Precise

:: MORE INFORMATION

Citation

PRECISE: software for prediction of cis-acting regulatory elements.
Trindade LM, van Berloo R, Fiers M, Visser RG.
J Hered. 2005 Sep-Oct;96(5):618-22. Epub 2005 Aug 31.

RNAAnalyzer – Identify Regulatory RNA Elements

RNAAnalyzer

:: DESCRIPTION

RNAAnalyzer is an integrated tool-box to identify regulatory RNA elements. The RNA analyzer collects general and specific information on any submitted RNA sequence or batch of sequences in FASTA format. It determines and rapidly scans the different regions of an RNA (including 5′ UTR, CDS, 3′ UTR in mRNA) and screens for specific RNA signals (in each of these regions, e.g. polyA-site, AU rich region etc. in 3′ UTR). It runs a fast folding RNA routine to provide an overview of the RNA fold. Furthermore it analyzes structure content, fold energy and stem loops.

::DEVELOPER

the Department of Bioinformatics at the University of Würzburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Peter Bengert and Thomas Dandekar
A software tool-box for analysis of regulatory RNA elements
Nucl. Acids. Res. 2003 31: 3441-3445.