title: Cactus: Algorithms for genome multiple sequence alignment.
abstract: Much attention has been given to the problem of creating reliable multiple sequence alignments in a model incorporating substitutions, insertions, and deletions. Far less attention has been paid to the problem of optimizing alignments in the presence of more general rearrangement and copy number variation. Using Cactus graphs, recently introduced for representing sequence alignments, we describe two complementary algorithms for creating genomic alignments. We have implemented these algorithms in the new "Cactus" alignment program. We test Cactus using the Evolver genome evolution simulator, a comprehensive new tool for simulation, and show using these and existing simulations that Cactus significantly outperforms all of its peers. Finally, we make an empirical assessment of Cactus's ability to properly align genes and find interesting cases of intra-gene duplication within the primates.
authors.affiliation: Center for Biomolecular Science and Engineering, University of California-Santa Cruz, CA 95064, USA. benedict@soe.ucsc.edu
authors.forename: Benedict
authors.initials: B
authors.lastname: Paten
authors.forename: Dent
authors.initials: D
authors.lastname: Earl
authors.forename: Ngan
authors.initials: N
authors.lastname: Nguyen
authors.forename: Mark
authors.initials: M
authors.lastname: Diekhans
authors.forename: Daniel
authors.initials: D
authors.lastname: Zerbino
authors.forename: David
authors.initials: D
authors.lastname: Haussler
mesh_terms: D000465:Algorithms; D000818:Animals; D003198:Computer Simulation; D023281:Genomics; D006801:Humans; D051379:Mice; D011323:Primates; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software