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The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates

Laurence Ettwiller1, Benedict Paten1, Marcel Souren2, Felix Loosli2, Jochen Wittbrodt2 and Ewan Birney1*

Author Affiliations

1 EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK

2 EMBL, Meyerhofstrasse, 69012 Heidelberg, Germany

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Genome Biology 2005, 6:R104  doi:10.1186/gb-2005-6-12-r104

Published: 2 December 2005

Abstract

We have developed several new methods to investigate transcriptional motifs in vertebrates. We developed a specific alignment tool appropriate for regions involved in transcription control, and exhaustively enumerated all possible 12-mers for involvement in transcription by virtue of their mammalian conservation. We then used deeper comparative analysis across vertebrates to identify the active instances of these motifs. We have shown experimentally in Medaka fish that a subset of these predictions is involved in transcription.