ArticleGenome research2003
AVID: A global alignment program.
Article in Genome research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 164 papers.
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Who cites it
164 citing papers in PubMed.
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- Comparative genomics, microsynteny, ancestral state reconstruction and selection pressure analysis across distinctive genomes and sub-genomes of Brassicaceae for analysis of evolutionary history ofPhysiology and molecular biology of plants : an international journal of functional plant biology · 2023Article
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- Multiple genome alignment in the telomere-to-telomere assembly era.Genome biology · 2022Review
- Comprehensive analysis of 1R- and 2R-MYBs reveals novel genic and protein features, complex organisation, selective expansion and insights into evolutionary tendencies.Functional & integrative genomics · 2022Article
- A Python-based programming language for high-performance computational genomics.Nature biotechnology · 2021Article
- A prescient evolutionary model for genesis, duplication and differentiation of MIR160 homologs in Brassicaceae.Molecular genetics and genomics : MGG · 2021Article
- The Genomes of Two Billfishes Provide Insights into the Evolution of Endothermy in Teleosts.Molecular biology and evolution · 2021Article
- GSAlign: an efficient sequence alignment tool for intra-species genomes.BMC genomics · 2020Article
- Comparative genomics reveals origin of MIR159A-MIR159B paralogy, and complexities of PTGS interaction between miR159 and target GA-MYBs in Brassicaceae.Molecular genetics and genomics : MGG · 2019Article
- Whole-Genome Alignment and Comparative Annotation.Annual review of animal biosciences · 2019Review
- Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points.Bioinformatics (Oxford, England) · 2019Article
- Taxogenomics and Systematics of the GenusFrontiers in microbiology · 2019Article
- Microsynteny analysis to understand evolution and impact of polyploidization on MIR319 family within Brassicaceae.Development genes and evolution · 2018Article
- Spatio-temporal expression dynamics differ between homologues of flowering time genes in the allopolyploid Brassica napus.The Plant journal : for cell and molecular biology · 2018Article
104 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
In this paper we describe a new global alignment method called AVID. The method is designed to be fast, memory efficient, and practical for sequence alignments of large genomic regions up to megabases long. We present numerous applications of the method, ranging from the comparison of assemblies to alignment of large syntenic genomic regions and whole genome human/mouse alignments. We have also performed a quantitative comparison of AVID with other popular alignment tools. To this end, we have established a format for the representation of alignments and methods for their comparison. These formats and methods should be useful for future studies. The tools we have developed for the alignment comparisons, as well as the AVID program, are publicly available. See Web Site References section for AVID Web address and Web addresses for other programs discussed in this paper.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.