MAVID: Constrained Ancestral Alignment of Multiple Sequences Export

@article{citeulike:2407068, abstract = {10.1101/gr.1960404 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.}, author = {Bray, Nicolas and Pachter, Lior}, citeulike-article-id = {2407068}, citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.1960404}, citeulike-linkout-1 = {http://genome.cshlp.org/content/14/4/693.abstract}, citeulike-linkout-2 = {http://genome.cshlp.org/content/14/4/693.full.pdf}, citeulike-linkout-3 = {http://www.genome.org/cgi/content/abstract/14/4/693}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/15060012}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=15060012}, day = {1}, doi = {10.1101/gr.1960404}, journal = {Genome Research}, keywords = {alignment, constrained, msa, pachtor}, month = {April}, number = {4}, pages = {693--699}, posted-at = {2009-05-23 05:28:12}, priority = {2}, title = {MAVID: Constrained Ancestral Alignment of Multiple Sequences}, url = {http://dx.doi.org/10.1101/gr.1960404}, volume = {14}, year = {2004} }

TY - JOUR ID - citeulike:2407068 L3 - citeulike-article-id:2407068 N2 - 10.1101/gr.1960404 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. IS - 4 JF - Genome Research EP - 699 TI - MAVID: Constrained Ancestral Alignment of Multiple Sequences VL - 14 SP - 693 KW - alignment KW - constrained KW - msa KW - pachtor AU - Bray, Nicolas AU - Pachter, Lior PY - 2004/04/01/ UR - http://dx.doi.org/10.1101/gr.1960404 ER -