Combining statistical alignment and phylogenetic footprinting to detect regulatory elements.

Journal article

MOTIVATION: Traditional alignment-based phylogenetic footprinting approaches make predictions on the basis of a single assumed alignment. The predictions are therefore highly sensitive to alignment errors or regions of alignment uncertainty. Alternatively, statistical alignment methods provide a framework for performing phylogenetic analyses by examining a distribution of alignments. RESULTS: We developed a novel algorithm for predicting functional elements by combining statistical alignment...

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Authors: Satija, R; Pachter, L; Hein, J

• Publication status: Published
• Journal: Bioinformatics (Oxford, England)
• Volume: 24
• Issue: 10
• Pages: 1236-1242
• Publication date: 2008-05-01
• DOI: 10.1093/bioinformatics/btn104
• EISSN: 1367-4811
• ISSN: 1367-4803
• Language: English
• Keywords: Regulatory Sequences, Nucleic Acid; Sequence Analysis, DNA; Base Sequence; Software; Data Interpretation, Statistical; DNA Footprinting; Sequence Alignment; Phylogeny; Molecular Sequence Data; Algorithms