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Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W613-6.

AliWABA: alignment on the web through an A-Bruijn approach.

Jones NC, Zhi D, Raphael BJ.

Source

Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA. ncjones@cs.uscd.edu

Abstract

Multiple sequence alignment programs are an invaluable tool in computational biology. A-Bruijn Alignment (ABA) is a method for multiple sequence alignment that represents an alignment as a directed graph and has proved useful in aligning nucleotide and amino acid sequences that are composed of repeated and shuffled subsequences. AliWABA is a web server that provides tools to generate alignments with ABA, visualize the resulting ABA graphs and extract subsequences from ABA graphs. AliWABA greatly simplifies the problem of analyzing multiple sequences for local similarities that may be reordered, as is common with the domain architectures of proteins. To facilitate the analysis of protein domains, AliWABA provides direct querying of the Conserved Domain Database. Availability: http://aba.nbcr.net/

PMID:: 16845083; [PubMed - indexed for MEDLINE]
PMCID: PMC1538870

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Publication Types, MeSH Terms, Substances

Publication Types

Research Support, Non-U.S. Gov't

MeSH Terms

Substances

POU Domain Factors

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Other Literature Sources

Labome Researcher Resource - ExactAntigen/Labome

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AliWABA - Bioinformatics.ca Links Directory

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