BoBro 2.1 – Identifying cis Regulatory Motifs in Prokaryotes

BoBro 2.1

:: DESCRIPTION

BoBro (BOTTLENECK BROKEN TOOL) is a software for prediction of cis-regulatory motifs in a given set of promoter sequences.

::DEVELOPER

Qin Ma , Bioinformatic and Mathematical Biosciences Lab, The Ohio State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOs/ Windows

:: DOWNLOAD

BoBro

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Sep 15;29(18):2261-8. doi: 10.1093/bioinformatics/btt397. Epub 2013 Jul 10.
An integrated toolkit for accurate prediction and analysis of cis-regulatory motifs at a genome scale.
Ma Q1, Liu B, Zhou C, Yin Y, Li G, Xu Y.

Nucleic Acids Res. 2011 Apr;39(7):e42. Epub 2010 Dec 11.
A new framework for identifying cis-regulatory motifs in prokaryotes.
Li G, Liu B, Ma Q, Xu Y.

GibbsModule – Multispecies de novo Identification of Cis-regulatory Motifs and Modules

GibbsModule

:: DESCRIPTION

GibbsModule is a software for de novo detection of cis-regulatory motifs and modules in eukaryote genomes. GibbsModule models the coexpressed genes within one species as sharing a core cis-regulatory motif and each homologous gene group as sharing a homologous cis-regulatory module (CRM), characterized by a similar composition of motifs.

::DEVELOPER

Zhong Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX

:: DOWNLOAD

GibbsModule

:: MORE INFORMATION

Citation

Genome Res. 2008 Aug;18(8):1325-35. Epub 2008 May 15.
Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells.
Xie D, Cai J, Chia NY, Ng HH, Zhong S.

MotifCombinator – Search for Combinations of Cis-regulatory Motifs

MotifCombinator

:: DESCRIPTION

MotifCombinator is an online tool with a user-friendly interface to systematically search for combinations composed of any number of motifs based on regression methods.

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Mar 22;8:100.
MotifCombinator: a web-based tool to search for combinations of cis-regulatory motifs.
Kato M1, Tsunoda T.