MAVID: constrained ancestral alignment of multiple sequences.
We describe a new global multiple-alignment program capable of aligning a large number of genomic regions. Our progressive-alignment approach incorporates the following ideas: maximum-likelihood inference of ancestral sequences, automatic guide-tree construction, protein-based anchoring of ab-initio gene predictions, and constraints derived from a global homology map of the sequences. We have implemented these ideas in the MAVID program, which is able to accurately align multiple genomic regions up to megabases long. MAVID is able to effectively align divergent sequences, as well as incomplete unfinished sequences. We demonstrate the capabilities of the program on the benchmark CFTR region, which consists of 1.8 Mb of human sequence and 20 orthologous regions in marsupials, birds, fish, and mammals. Finally, we describe two large MAVID alignments, an alignment of all the available HIV genomes and a multiple alignment of the entire human, mouse, and rat genomes.
Bray
Nicolas
N
Department of Mathematics, University of California at Berkeley, Berkeley, California 94720, USA.
Pachter
Lior
L
D000818:Animals; D002415:Cats; D002417:Cattle; D019295:Computational Biology / Q000379:methods; D019005:Cystic Fibrosis Transmembrane Conductance Regulator / Q000235:genetics; D004285:Dogs; D019143:Evolution, Molecular; D005399:Fishes / Q000235:genetics; D016678:Genome; D015894:Genome, Human; D016679:Genome, Viral; D015497:HIV-1 / Q000235:genetics; D006801:Humans; D051379:Mice; D011817:Rabbits; D051381:Rats; D016415:Sequence Alignment / Q000379:methods* / Q000706:statistics & numerical data; D015302:Simian Immunodeficiency Virus / Q000235:genetics; D012984:Software / Q000706:statistics & numerical data / Q000639:trends*; D013552:Swine / Q000235:genetics
C505032:CFTR protein, human; D019005:Cystic Fibrosis Transmembrane Conductance Regulator