CompMoby: Comparative MobyDick for detection of cis-regulatory motifs

Background: The regulation of gene expression is complex and occurs at many levels, including transcriptional and post-transcriptional, in metazoans. Transcriptional regulation is mainly determined by sequence elements within the promoter regions of genes while sequence elements within the 3' untranslated regions of mRNAs play important roles in post-transcriptional regulation such as mRNA stability and translation efficiency. Identifying cis-regulatory elements, or motifs, in multicellular eukaryotes is more difficult compared to unicellular eukaryotes due to the larger intergenic sequence space and the increased complexity in regulation. Experimental techniques for discovering functional elements are often time consuming and not easily applied on a genome level. Consequently, computational methods are advantageous for genome-wide cis-regulatory motif detection. To decrease the search space in metazoans, many algorithms use cross-species alignment, although studies have demonstr...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Christina Chaivorapol, Collin Melton, Grace Wei, Ru-Fang Yeh, Miguel Ramalho-Santos, Robert Blelloch, Hao Li
• Keywords: Binding Sites, BMCBI 2008, Cis-regulatory, Cis-regulatory Elements