Tag: Phylogenetic Footprinting

ORCAtk 1.0.0 – Transcription Factor Binding Site Detection using Phylogenetic Footprinting

ORCAtk 1.0.0

:: DESCRIPTION

The ORCA Toolkit is a system for finding putative regulatory regions and transcription factor binding sites (TFBSs) within those regions.

::DEVELOPER

The Wasserman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • Perl

:: DOWNLOAD

 ORCAtk

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 Jan;37(Database issue):D54-60. doi: 10.1093/nar/gkn783. Epub 2008 Oct 29.
The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences.
Portales-Casamar E, Arenillas D, Lim J, Swanson MI, Jiang S, McCallum A, Kirov S, Wasserman WW.

ConSite – Transcription Factor Binding Site Detection using Phylogenetic Footprinting

ConSite

:: DESCRIPTION

ConSite explores transcription factor binding sites shared by two genomic sequences

::DEVELOPER

The Wasserman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W249-52.
ConSite: web-based prediction of regulatory elements using cross-species comparison.
Sandelin A, Wasserman WW, Lenhard B.

BigFoot – Bayesian Alignment and Phylogenetic Footprinting with MCMC

BigFoot

:: DESCRIPTION

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC. Annotates the locations of conserved elements in multiple sequence while correcting for alignment uncertainty and error.

::DEVELOPER

Rahul Satija

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Java

:: DOWNLOAD

 BigFoot

:: MORE INFORMATION

Citation

BMC Evol Biol. 2009 Aug 28;9:217.
BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC.
Satija R, Novák A, Miklós I, Lyngs? R, Hein J.

FootPrinter 2.1 / MicroFootPrinter – Phylogenetic Footprinting

FootPrinter 2.1

:: DESCRIPTION

FootPrinter is a program for phylogenetic footprinting. Phylogenetic footprinting is a method that identifies putative regulatory elements in DNA sequences. It identifies regions of DNA that are unusually well conserved across a set of orthologous sequences.

FootPrinter Web version

MicroFootPrinter is a front end to the FootPrinter phylogenetic footprinting program, but with specific focus on prokaryotic genomes. You supply a prokaryotic species and gene of interest, and you set a few parameters (or leave them at their default values). MicroFootPrinter will then find related prokaryotes containing a homologous gene, and run FootPrinter to identify motifs that are well conserved across the cis-regulatory regions of these homologous genes.

MicroFootPrinter Web Version

::DEVELOPER

The Computational & Synthetic Biology group – COMPUTER SCIENCE & ENGINEERING at UNIVERSITY OF WASHINGTON

:: SCREENSHOTS

FootPrinter

MicroFootPrinter

:: REQUIREMENTS

:: DOWNLOAD

FootPrinter Source Code ; Manual

:: MORE INFORMATION

Citation for FootPrinter:

  • M. Blanchette, B. Schwikowski, M. Tompa, “Algorithms for phylogenetic footprinting”, J. Comput. Biol., vol. 9 (2002) 211-23. Pubmed 12015878.
  • M. Blanchette, M. Tompa, “Discovery of regulatory elements by a computational method for phylogenetic footprinting”, Genome Res., vol. 12 (2002) 739-48.Pubmed 11997340.   Supplement.
  • M. Blanchette, M. Tompa, “FootPrinter: A program designed for phylogenetic footprinting”, Nucleic Acids Res., vol. 31 (2003) 3840-2. Pubmed 12824433.

Citation for MicroFootPrinter:

Exit mobile version