TargetOrtho 2.0 – A Phylogenetic Footprinting Tool to Identify Transcription Factor Targets

TargetOrtho 2.0

:: DESCRIPTION

TargetOrtho provides a cost- and time-efficient in silico approach for the identification of novel TF target genes, and, together with its CRM search function, is poised to unravel the regulatory logic of diverse biological processes.

::DEVELOPER

Hobert Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

TargetOrtho

:: MORE INFORMATION

Citation

Genetics. 2014 May;197(1):61-76. doi: 10.1534/genetics.113.160721. Epub 2014 Feb 20.
TargetOrtho: a phylogenetic footprinting tool to identify transcription factor targets.
Glenwinkel L1, Wu D, Minevich G, Hobert O.

FOOTER 2.0 – Find Ammalian Transcription Factor Binding Sites using Phylogenetic Footprinting

FOOTER 2.0

:: DESCRIPTION

FOOTER analyses a pair of homologous mammalian DNA sequences (i.e. human and mouse/rat) for high probability binding sites of known transcription factors. A set of Position-Specific Scoring Matrices (PSSM) has been carefully constructed from mammalian transcription factor binding sites deposited in TRANSFAC database.

::DEVELOPER

Benos Lab

SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting.
Corcoran DL, Feingold E, Benos PV.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W442-6.