Multiple organism algorithm for finding ultraconserved elements

Background: Ultraconserved elements are nucleotide or protein sequences with 100% identity (no mismatches, insertions, or deletions) in the same organism or between two or more organisms. Studies indicate that these conserved regions are associated with micro RNAs, mRNA processing, development and transcription regulation. The identification and characterization of these elements among genomes is necessary for the further understanding of their functionality. Results: We describe an algorithm and provide freely available software which can find all of the ultraconserved sequences between genomes of multiple organisms. Our algorithm takes a combinatorial approach that finds all sequences without requiring the genomes to be aligned. The algorithm is significantly faster than BLAST and is designed to handle very large genomes efficiently. We ran our algorithm on several large comparative analyses to evaluate its effectiveness; one compared 17 vertebrate genomes where we find 123 ultracon...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Scott Christley, Neil F. Lobo, Gregory R. Madey
• Keywords: Algorithm, BMCBI 2008, Genome, Sequences