Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation
- 24 June 2007
- journal article
- Published by Springer Nature in Nature Methods
- Vol. 4 (7) , 563-565
- https://doi.org/10.1038/nmeth1061
Abstract
We developed Trawler, the fastest computational pipeline to date, to efficiently discover over-represented motifs in chromatin immunoprecipitation (ChIP) experiments and to predict their functional instances. When we applied Trawler to data from yeast and mammals, 83% of the known binding sites were accurately called, often with other additional binding sites, providing hints of combinatorial input. Newly discovered motifs and their features (identity, conservation, position in sequence) are displayed on a web interface.Keywords
This publication has 16 references indexed in Scilit:
- An improved map of conserved regulatory sites for Saccharomyces cerevisiaeBMC Bioinformatics, 2006
- A new generation of JASPAR, the open-access repository for transcription factor binding site profilesNucleic Acids Research, 2006
- TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotesNucleic Acids Research, 2006
- The discovery, positioning and verification of a set of transcription-associated motifs in vertebratesGenome Biology, 2005
- T-Reg Comparator: an analysis tool for the comparison of position weight matricesNucleic Acids Research, 2005
- TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysisNucleic Acids Research, 2005
- Assessing computational tools for the discovery of transcription factor binding sitesNature Biotechnology, 2005
- Transcriptional regulatory code of a eukaryotic genomeNature, 2004
- Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genesNucleic Acids Research, 2004
- The Jalview Java alignment editorBioinformatics, 2004