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Published online before print December 30, 2002, 10.1101/gr.789803
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Vol 13, Issue 1, 97-102, January 2003

METHODS

AVID: A Global Alignment Program

Nick Bray1,2, Inna Dubchak1 and Lior Pachter2,3

1Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; 2Department of Mathematics, University of California, Berkeley, California 94720, USA

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.

3 Corresponding author.

E-MAIL lpachter{at}math.berkeley.edu; FAX (510) 642-8204.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.789803. Article published online before print in December 2002.


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[Abstract] [Full Text] [PDF]

Home page
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[Abstract] [Full Text] [PDF]

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[Abstract] [Full Text] [PDF]

Home page
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[Abstract] [Full Text] [PDF]

Home page
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[Full Text] [PDF]

Home page
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[Abstract] [Full Text] [PDF]

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[Abstract] [Full Text] [PDF]

Home page
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