AVID: A global alignment program.

By Nicholas L. Bray, Inna Dubchak, Lior S. Pachter. Genome Research, 2003

527 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/3b8cae94872aafb65bed2829d02f3aedd733ee7e

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Citations in the corpus

Algebraic Statistics for Computational Biology: Preface (2005, methodology): “Popular alignment programs include pairwise aligners such as AVID [Bray et al., 2003] and BLASTZ [Schwartz et al.”
VISTA: computational tools for comparative genomics (2004, methodology): “…(7) the user sub-mits a single sequence (draft or ﬁnished) which is compared with publicly available completed whole-genome assemblies. mVISTA (4,6) is the original program, designed for comparison of orthologous sequences of different species. rVISTA (9) combines a transcription factor binding…”
African community-based conservation: a systematic review of social and ecological outcomes (2018, background): “…win-win solutions, there is little empirical evidence that supports enhanced conservation and development, especially in Africa (Songorwa et al. 2000, Bray et al. 2003, Blaikie 2006, Duffy 2006, Kothari 2006, Berkes 2007, Hoole 2007, Seixas and Davy 2008, Roe et al. 2009, Awung and Marchant 2016).”
Transcriptional regulation by calcium, calcineurin, and NFAT. (2003, background): “These regions often (but not always) correspond to highly conserved noncoding sequences (CNS) identified by comparing the sequences of gene loci in two or more mammalian genomes using Web-based programs such as VISTA (Mayor et al. 2000; Loots et al. 2002; Bray et al. 2003) or PipMaker (Schwartz et a”
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory (2012, methodology): “The relationship between many existing alignment methods [1,3-5,10-23] is qualitatively illustrated in Figure 1.”
GMAP: a genomic mapping and alignment program for mRNA and EST sequence (2005, methodology): “A procedure for identifying microexons has been developed by Volfovskyet al. (2003), and applied in a large-scale study.”
Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. (2008, background): “The second problem has been handled by different types of constraint heuristics, mostly relying on finding confident regions of high similarity that can be detected using more aggressive methods (Bray et al. 2003; Kurtz et al. 2004).”
Principles of MicroRNA–Target Recognition (2005, methodology): “These 39 UTR sequences were then aligned to the D. melanogaster and D. pseudoobscura 39 UTRs using AVID. miRNA-sequences.”
A survey of DNA motif finding algorithms (2007, methodology): “They compared the performance of CONREAL with two global alignment programs LAGAN [64] and AVID [65] using a reference data set and observed that CONREAL worked equally well for closely related species like rodent and human and has a clear added value for aligning promoter elements of more divergent”
Principles of MicroRNATarget Recognition (2005, methodology): “3′ adjacent sequence (Human Genome Sequencing Center at Baylor College of Medicine) using AVID [”
Computational identification of microRNA targets (2004, methodology): “To define the homologous Drosophila pseudoobscura 3 UTR sequences we used the Berkeley genome pipeline (Couronne et al., 2003; Bray et al., 2003) website (pipeline.lbl.gov/pseudo/) which presents a genomic alignment of the two species.”
Versatile and open software for comparing large genomes (2004, background): “Since the development of MUMmer 1.0 in 1999, several other programs for large-scale genome comparison have been developed, for example, SSAHA [16], AVID [17], MGA [18], BLASTZ [19], and LAGAN [20] (see also [21] for a review).”
Computational identification of Drosophila microRNA genes (2003, methodology): “These contigs were aligned to the first assembly of the D. pseudoobscura euchromatic sequence [37] by running 1287 parallel AVID jobs on the Linux cluster.”
MicroRNA targets in Drosophila (2003, methodology): “The AVID [46] alignment tool was used to align the real D. melanogaster 3' UTR and a candidate D. pseudoobscura region.”
Human MicroRNA Targets (2004, methodology): “Pairs of orthologous UTRs were aligned with each other using the AVID (Bray et al. 2003) alignment algorithm to facilitate analysis of conservation of position and sequence of target sites.”