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Published online before print June 3, 2008, 10.1101/gr.076117.108
Genome Res. 18:1180-1189, 2008
©2008 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/08 $5.00
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Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets

Chaim Linhart1, Yonit Halperin1, and Ron Shamir2

School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel

We present a threefold contribution to the computational task of motif discovery, a key component in the effort of delineating the regulatory map of a genome: (1) We constructed a comprehensive large-scale, publicly-available compendium of transcription factor and microRNA target gene sets derived from diverse high-throughput experiments in several metazoans. We used the compendium as a benchmark for motif discovery tools. (2) We developed Amadeus, a highly efficient, user-friendly software platform for genome-scale detection of novel motifs, applicable to a wide range of motif discovery tasks. Amadeus improves upon extant tools in terms of accuracy, running time, output information, and ease of use and is the only program that attained a high success rate on the metazoan compendium. (3) We demonstrate that by searching for motifs based on their genome-wide localization or chromosomal distributions (without using a predefined target set), Amadeus uncovers diverse known phenomena, as well as novel regulatory motifs.

1 These authors contributed equally to this work.

2 Corresponding author.

E-mail rshamir{at}tau.ac.il; fax 972-3-640-5384.

[Supplemental material is available online at www.genome.org. The Amadeus software is available at http://acgt.cs.tau.ac.il/amadeus.]

Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.076117.108.


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