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This article is part of the supplement: Proceedings of the Tenth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics

Open Access Proceedings

Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites

Mathieu Blanchette

Author Affiliations

McGill Centre for Bioinformatics and School of Computer Science, McGill University, H3C 2B4, Québec, Canada

This work was carried out in part while on sabbatical at the Laboratoire d'Informatique, Robotique, et Microélectronique de Montpellier (Université Montpellier 2), 161 rue Ada, Montpellier, France

BMC Bioinformatics 2012, 13(Suppl 19):S2  doi:10.1186/1471-2105-13-S19-S2

Published: 19 December 2012

Additional files

Additional file 1:

Example of the GATA-1 binding sites predicted in each extant and ancestral sequences in the first exon of the NPL gene. A region bound by GATA-1, identified by ChIP-Seq, is located just upstream of the second (alternative) exon. Rows corresponding to ancestral sequences are identified by listing the names of the extant descendants of each ancestor. Panel B is a zoom on the high-scoring binding locus region. Note that the region does not exhibit elevated sequence conservation, and contains many examples of TFBS turnover.

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