Simultaneous alignment and annotation of cis-regulatory regions

Genomic transcriptional processes rely heavily on the combinatorial binding of transcription factors on the upstream regions of genes. Analysis and complete characterization of such ’regulatory’ regions can unlock the door to the understanding of regulatory and transcriptional mechanisms. Such analysis is usually based on the prediction of transcription factor binding site (TFBS) hits on non-coding regions. To improve the prediction of TFBS hits, phylogeneticfootprinting is generally employed. Here we propose a method that combines sequence comparison and scanning with TFBS hits to generate simultaneously annotated alignments. The hope is that simultaneous alignment and annotation can result in an improved specificity.

• Type: Journal
• Year: 2007
• Where: BIOINFORMATICS
• Authors: Abha Singh Bais, Steffen Grossmann, Martin Vingron
• Keywords: BIOINFORMATICS 2007, Genomic Transcriptional Processes, Transcription Factor, Upstream Regions