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AVID: A Global Alignment Program

Bray, Nick and Dubchak, Inna and Pachter, Lior (2003) AVID: A Global Alignment Program. Genome Research, 13 (1). pp. 97-102. ISSN 1088-9051. PMCID PMC430967. doi:10.1101/gr.789803. https://resolver.caltech.edu/CaltechAUTHORS:20170308-155631683

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1101/gr.789803DOIArticle
http://genome.cshlp.org/content/13/1/97.shortPublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430967/PubMed CentralArticle
ORCID:
AuthorORCID
Pachter, Lior0000-0002-9164-6231
Additional Information:© 2003 Cold Spring Harbor Laboratory Press. The Authors acknowledge that six months after the full-issue publication date, the Article will be distributed under a Creative Commons CC-BY-NC License (Attribution-NonCommercial 4.0 International License, http://creativecommons.org/licenses/by-nc/4.0/). Received September 9, 2002. Accepted November 7, 2002. We thank Alex Poliakov for helping in setting up the AVID Web servers and provided extensive debugging support and assistance. We also thank Jody Schwartz for help in testing and debugging AVID and Jim Lord who helped in developing overlap identification methods for draft contigs. Thanks also to the Mouse Sequencing Consortium for generating whole genome mouse sequence, which helped greatly in refining and streamlining AVID. Some of the sequence data used to benchmark the alignment programs were generated by the NIH Intramural Sequencing Center (www.nisc.nih.gov). This project was supported in part by a Program in Genomic Applications grant (PGA) from the National Heart Lung and Blood Institute and a grant from the NIH (R01-HG02362-01). The publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 USC section 1734 solely to indicate this fact.
Funders:
Funding AgencyGrant Number
NIHR01-HG02362-01
Issue or Number:1
PubMed Central ID:PMC430967
DOI:10.1101/gr.789803
Record Number:CaltechAUTHORS:20170308-155631683
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170308-155631683
Official Citation:AVID: A Global Alignment Program Nick Bray, Inna Dubchak, and Lior Pachter Genome Res. January 1, 2003 13: 97-102; Published in Advance December 30, 2002, doi:10.1101/gr.789803
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74943
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:09 Mar 2017 16:09
Last Modified:15 Nov 2021 16:29

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