Title: Finding functional promoter motifs by computational methods: a word of caution

Authors: Rajesh Chowdhary, Limsoon Wong, Vladimir B. Bajic

Addresses: Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613; School of Computing, National University of Singapore, 117543 Singapore. ' School of Computing, National University of Singapore, 117543 Singapore. ' Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613; South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa

Abstract: The standard practice in the analysis of promoters is to select promoter regions of convenient length. This may lead to false results when searching for Transcription Factor Binding Sites (TFBSs), since the sequences may contain coding segments. In such cases, motif detection may single out motifs from the coding regions. The mapping of TFBSs to promoters may result in a misleading picture of |promoter| content. We illustrate these issues using the example of histones H2A and H2B and show how such analysis could be misleading if care is not exercised to eliminate coding regions from the presumed promoter sequences.

Keywords: promoters; transcription start sites; TSS; translation initiation sites; TIS; transcription factor binding sites; TFBS; motifs; bioinformatics.

DOI: 10.1504/IJBRA.2006.010605

International Journal of Bioinformatics Research and Applications, 2006 Vol.2 No.3, pp.282 - 288

Published online: 07 Aug 2006 *

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