Multiple non-collinear TF-map alignments of promoter regions

Background: The analysis of the promoter sequence of genes with similar expression patterns is a basic tool to annotate common regulatory elements. Multiple sequence alignments are on the basis of most comparative approaches. The characterization of regulatory regions from coexpressed genes at the sequence level, however, does not yield satisfactory results in many occasions as promoter regions of genes sharing similar expression programs often do not show nucleotide sequence conservation. Results: In a recent approach to circumvent this limitation, we proposed to align the maps of predicted transcription factors (referred as TF-maps) instead of the nucleotide sequence of two related promoters, taking into account the label of the corresponding factor and the position in the primary sequence. We have now extended the basic algorithm to permit multiple promoter comparisons using the progressive alignment paradigm. In addition, non-collinear conservation blocks might now be identified i...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Enrique Blanco, Roderic Guigó, Xavier Messeguer
• Keywords: BMCBI 2007, Nucleotide Sequence, Promoter, Sequence Alignments