OWEN: aligning long collinear regions of genomes

Aleksey Y Ogurtsov; Mikhail A Roytberg; Svetlana A Shabalina; Alexey S Kondrashov

doi:10.1093/bioinformatics/18.12.1703

OWEN: aligning long collinear regions of genomes

Bioinformatics. 2002 Dec;18(12):1703-4. doi: 10.1093/bioinformatics/18.12.1703.

Authors

Aleksey Y Ogurtsov¹, Mikhail A Roytberg, Svetlana A Shabalina, Alexey S Kondrashov

Affiliation

¹ National Center for Biotechnology Information, NIH, 45 Center Drive, Bethesda, MD 20892-6510, USA. [email protected]

PMID: 12490463
DOI: 10.1093/bioinformatics/18.12.1703

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.

MeSH terms

Algorithms*
Base Sequence
Chromosomes, Human, 6-12 and X / genetics
Conserved Sequence / genetics
Databases, Nucleic Acid
Evolution, Molecular
Genome*
Humans
Information Storage and Retrieval / methods
Molecular Sequence Data
Sequence Alignment / methods*
Sequence Analysis, DNA / methods*
Sequence Homology, Nucleic Acid
Software