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

Neil C Jones; Degui Zhi; Benjamin J Raphael

doi:10.1093/nar/gkl288

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

Neil C Jones·Degui Zhi·Benjamin J Raphael

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Abstract

UNLABELLED: 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/

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Algorithms Amino Acid Sequence Base Sequence Computer Graphics Internet POU Domain Factors Protein Structure, Tertiary Sequence Alignment Software User-Computer Interface Journal Article Research Support, Non-U.S. Gov't

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Neil C Jones, Degui Zhi, Benjamin J Raphael. 2006-07-01. AliWABA: alignment on the web through an A-Bruijn approach.. https://doi.org/10.1093/nar%2Fgkl288

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