AVID: A Global Alignment Program | Zendy

Nicholas J. Bray | Zendy; Inna Dubchak | Zendy; Lior Pachter | Zendy

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AVID: A Global Alignment Program

Author(s) -

Nicholas J. Bray,

Inna Dubchak,

Lior Pachter

Publication year - 2002

Publication title -

genome research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.556

H-Index - 297

eISSN - 1549-5469

pISSN - 1088-9051

DOI - 10.1101/gr.789803

Subject(s) - biology , synteny , web site , multiple sequence alignment , sequence alignment , alignment free sequence analysis , computational biology , representation (politics) , computer science , sequence (biology) , web application , genome , information retrieval , genetics , world wide web , the internet , gene , peptide sequence , politics , political science , law

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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