Tag: Cis-Regulatory Element

CisRNA-SVM – Identification of Structured Cis-regulatory Elements in the 3’UTRs of human Protein-coding mRNAs

CisRNA-SVM

:: DESCRIPTION

CisRNA-SVM is a software for genome wide predictions of novel structured RNA cis-regulatory elements in human 3′ UTRs.

::DEVELOPER

Dr Chris Brown’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • Perl

:: DOWNLOAD

CisRNA-SVM

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2012 Oct;40(18):8862-73. doi: 10.1093/nar/gks684. Epub 2012 Jul 20.
Computational identification of new structured cis-regulatory elements in the 3′-untranslated region of human protein coding genes.
Chen XS1, Brown CM.

creDB 0.1.9 – Cis–REgulatory elements DataBase

creDB 0.1.9

:: DESCRIPTION

The creDB package provides easy access to a sqlite database containing enhancer sequences annotated across a range of biological contexts (tissues, cell types).

::DEVELOPER

Kostka Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R

:: DOWNLOAD

creDB

:: MORE INFORMATION

Citation

Genome-wide Enhancer Maps Differ Significantly in Genomic Distribution, Evolution, and Function.
ML Benton, SC Talipineni, D Kostka,
JA Capra BMC Genomics 2019.

CEAS 1.0.2 – Cis-regulatory Element Annotation System

CEAS 1.0.2

:: DESCRIPTION

CEAS (Cis-regulatory Element Annotation System) is a standalone Python package for analyzing ChIP-chip/seq data. The tool was designed to characterize genome-wide protein-DNA interaction patterns from ChIP-chip and ChIP-Seq of both sharp and broad binding factors. As a stand-alone extension of our web application CEAS , it provides statistics on ChIP enrichment at important genome features such as specific chromosome, promoters, gene bodies, or exons, and infers genes most likely to be regulated by a binding factor. CEAS also enables biologists to visualize the average ChIP enrichment signals over specific genomic features, allowing continuous and broad ChIP enrichment to be perceived which might be too subtle to detect from ChIP peaks alone.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CEAS

:: MORE INFORMATION

Citation:

Shin H, Liu T, Manrai AK, Liu XS.
CEAS: cis-regulatory element annotation system.
Bioinformatics. 2009 Oct 1;25(19):2605-6. Epub 2009 Aug 18.

StructRED – Structural Cis-Regulatory Element Detector

StructRED

:: DESCRIPTION

StructRED (Structural Cis-Regulatory Element Detector) is an alignment-free algorithm that discovers secondary structure-defined cis-regulatory elements in mRNAs by modeling the effects that their occurrences exert on quantitative measurements of mRNA behavior in the form of microarray data.

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

StructRED

:: MORE INFORMATION

Barrett Foat and Gary D. Stormo
Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs
Mol. Syst. Biol. 2009. 5:268.

JPREdictor 1.23 – Predict Cis-regulatory Elements

JPREdictor 1.23

:: DESCRIPTION

jPREdictor is a tool for the prediction of cis-regulatory elements, e.g. PRE/TREs in Drosophila melanogaster. Short sequence fragments, namely transcription factor binding sites, are known to be enriched and clustered in such elements. These binding sites are represented as motifs and for the prediction, they must be known. Using these motifs, it is possible to search them on sequences, to weight them by applying a positive or negative training set (model or background, respectively) and to score a sequence.

::DEVELOPER

Thomas Fiedler & Marc Rehmsmeier

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

JPREdictor

:: MORE INFORMATION

Citation

Thomas Fiedler
The jPREdictor and its Application to Motif Discovery, Motif Clustering and the Prediction of Polycomb/Trithorax Response Elements
Dissertation, Univerity of Bielefeld, Apr 2008

Thomas Fiedler and Marc Rehmsmeier
jPREdictor: a versatile tool for the prediction of cis-regulatory elements
Nucleic Acids Research, 34:W546-W550, 2006

Cistematic 3.0 – Platform for Cis-regulatory Element Analysis

Cistematic 3.0

:: DESCRIPTION

Cistematic is a Python package with a rich set of API’s that simplify the collection and analysis of candidate cis-regulatory elements from a number of different motif-finding programs such as Meme, and cisGreedy (built-in). Cistematic assesses the significance of each motif by comparing it to its prevalence genome-wide.

::DEVELOPER

the Wold Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsx/WIndows with Cygwin
  • Python

:: DOWNLOAD

  Cistematic

:: MORE INFORMATION

Citation:

Genome Res. 2006 Oct;16(10):1208-21. Epub 2006 Sep 8.
Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire.
Mortazavi A, Leeper Thompson EC, Garcia ST, Myers RM, Wold B.

creto 1.0 – Determination of Cis-Regulatory Element Turn-Over rates

creto 1.0

:: DESCRIPTION

creto (Cis-Regulatory Element Turn-Over) is a program for the determination of the evolutionary origination and decay rates of transcription factor binding sites. Given a phylogenetic tree and the binding site numbers of the species at the tips, creto uses a maximum likelihood model that permits variable turnover rates in different parts of the species tree. This model can be used to detect changes in turnover rate as a proxy for differences in the selective pressures acting on TFBS in different clades.

::DEVELOPER

Wolfgang Otto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 creto

:: MORE INFORMATION

Citation

Otto W, Stadler PF, Lopez-Gialdez F, Townsend JP, Lynch VJ, Wagner GP
Measuring Transcription Factor Binding Site Turnover: A Maximum Likelihood Approach using Phylogenies.
Genome Biol Evol. 2009 May 25;1:85-98.