PriorsEditor: a tool for the creation and use of positional priors in motif discovery.

Bioinformatics
Kjetil Klepper, Finn Drabløs

Abstract

Computational methods designed to discover transcription factor binding sites in DNA sequences often have a tendency to make a lot of false predictions. One way to improve accuracy in motif discovery is to rely on positional priors to focus the search to parts of a sequence that are considered more likely to contain functional binding sites. We present here a program called PriorsEditor that can be used to create such positional priors tracks based on a combination of several features, including phylogenetic conservation, nucleosome occupancy, histone modifications, physical properties of the DNA helix and many more. PriorsEditor is available as a web start application and downloadable archive from http://tare.medisin.ntnu.no/priorseditor (requires Java 1.6). The web site also provides tutorials, screenshots and example protocol scripts.

References

Jun 1, 1997·Current Opinion in Structural Biology·L Duret, P Bucher
May 17, 2000·Bioinformatics·G D Stormo
Apr 3, 2004·Genome Research·Diana KolbeFrancesca Chiaromonte
May 8, 2004·Nature Reviews. Genetics·Wyeth W Wasserman, Albin Sandelin
Dec 31, 2005·Nucleic Acids Research·V MatysE Wingender
Apr 8, 2006·Biology Direct·Geir Kjetil Sandve, Finn Drabløs
Jul 25, 2006·Nature·Eran SegalJonathan Widom
Jul 29, 2006·Bioinformatics·Leelavati NarlikarAlexander J Hartemink
Nov 17, 2007·Nucleic Acids Research·Obi L GriffithUNKNOWN Open Regulatory Annotation Consortium
Mar 28, 2008·PloS One·Harri LähdesmäkiIlya Shmulevich
Nov 13, 2009·Nucleic Acids Research·Elodie Portales-CasamarAlbin Sandelin
Nov 13, 2009·Nucleic Acids Research·Brooke RheadW James Kent
Mar 10, 2010·Cell·Timothy RavasiYoshihide Hayashizaki
Apr 13, 2010·BMC Bioinformatics·Timothy L BaileyPhilip Machanick

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Methods Mentioned

BETA
ChIP-chip
ChIP-seq

Software Mentioned

PriorsEditor
PRIORITY
ORegAnno
UCSC Genome Browser

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