title: OWEN: aligning long collinear regions of genomes.
abstract: OWEN is an interactive tool for aligning two long DNA sequences that represents similarity between them by a chain of collinear local similarities. OWEN employs several methods for constructing and editing local similarities and for resolving conflicts between them. Alignments of sequences of lengths over 10(6) can often be produced in minutes. OWEN requires memory below 20 L, where L is the sum of lengths of the compared sequences.
authors.affiliation: National Center for Biotechnology Information, NIH, 45 Center Drive, Bethesda, MD 20892-6510, USA. ogurtsov@ncbi.nlm.nih.gov
authors.forename: Aleksey Y
authors.initials: AY
authors.lastname: Ogurtsov
authors.forename: Mikhail A
authors.initials: MA
authors.lastname: Roytberg
authors.forename: Svetlana A
authors.initials: SA
authors.lastname: Shabalina
authors.forename: Alexey S
authors.initials: AS
authors.lastname: Kondrashov
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002906:Chromosomes, Human, 6-12 and X / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D016678:Genome; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software