ArticleGenome research2004
MAVID: constrained ancestral alignment of multiple sequences.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 121 papers.
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Who cites it
121 citing papers in PubMed, 293 citations in OpenAlex.
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- Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments.Molecular biology and evolution · 2019Article
- Accurate high throughput alignment via line sweep-based seed processing.Nature communications · 2019Article
- Conserved Critical Evolutionary Gene Structures in Orthologs.Journal of molecular evolution · 2019Article
- Development and Evaluation of a Novel Loop-Mediated Isothermal Amplification Assay for Diagnosis of Cutaneous and Visceral Leishmaniasis.Journal of clinical microbiology · 2018Article
- Coordinate systems for supergenomes.Algorithms for molecular biology : AMB · 2018Article
- Alternative Splicing within and between Drosophila Species, Sexes, Tissues, and Developmental Stages.PLoS genetics · 2016Article
- Circular sequence comparison: algorithms and applications.Algorithms for molecular biology : AMB · 2016Article
- Identification and computational analysis of gene regulatory elements.Cold Spring Harbor protocols · 2015Review
- Rapid diversification of five Oryza AA genomes associated with rice adaptation.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- The evolution of comparative genomics.Molecular genetics & genomic medicine · 2014Article
- PSAR-align: improving multiple sequence alignment using probabilistic sampling.Bioinformatics (Oxford, England) · 2014Article
- cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila.BMC systems biology · 2014Article
- The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.Genome biology · 2014Article
- An alignment-free test for recombination.Bioinformatics (Oxford, England) · 2013Article
61 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
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.
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