AVID: A Global Alignment Program
- Creators
- Bray, Nick
- Dubchak, Inna
-
Pachter, Lior
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.
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.Attached Files
Published - 97.full.pdf
Files
| Name | Size | Download all |
|---|---|---|
|
md5:3fc4f818a092fb6cac28b625c7585f28
|
254.4 kB | Preview Download |
Additional details
- PMCID
- PMC430967
- Eprint ID
- 74943
- Resolver ID
- CaltechAUTHORS:20170308-155631683
- R01-HG02362-01
- NIH
- Created
-
2017-03-09Created from EPrint's datestamp field
- Updated
-
2021-11-15Created from EPrint's last_modified field