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Genome Res. 2008 Jul;18(7):1180-9. doi: 10.1101/gr.076117.108. Epub 2008 Apr 14.

Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets.

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  • 1School 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.

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