title: Pattern-constrained multiple polypeptide sequence alignment.
abstract: Multiple sequence alignment (MSA) is one of the fundamental research topics in computational biology. The alignments help us to find functional assignment, evolutionary history and conserved region. Previous methods use a substitution matrix and do not incorporate knowledge of the sequences being aligned. Therefore, they do not assure the alignment of similar structures and common patterns in the sequences. We have been investigating into the solution to the problem in multiple and making use of knowledge of the sequences being aligned, including patterns in the Prosite databank, Blocks+, eBlocks databases, as well as motif and structural information. A pattern-constrained algorithm has been developed. Experiments with protein sequences have shown more accurate alignments with incorporation of the domain knowledge available in the sequences.
authors.affiliation: BioInformatics Research Centre, Nanyang Technological University, Nanyang Avenue, Singapore 639798, Singapore. duzhihua@pmail.ntu.edu.sg
authors.forename: Zhihua
authors.initials: Z
authors.lastname: Du
authors.forename: Feng
authors.initials: F
authors.lastname: Lin
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D019992:Databases as Topic; D005786:Gene Expression Regulation; D006801:Humans; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*
chemical_list: D010455:Peptides