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

TitleAliWABA: alignment on the web through an A-Bruijn approach.
Publication TypeJournal Article
Year of Publication2006
AuthorsJones NC, Zhi D, Raphael BJ
JournalNucleic Acids Res
Volume34
IssueWeb Server issue
PaginationW613-6
Date Published2006 Jul 1
ISSN1362-4962
KeywordsAlgorithms, Amino Acid Sequence, Base Sequence, Computer Graphics, Internet, POU Domain Factors, Protein Structure, Tertiary, Sequence Alignment, Software, User-Computer Interface
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/

DOI10.1093/nar/gkl288
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/16845083?dopt=Abstract
PMCPMC1538870
Alternate JournalNucleic Acids Res.
PubMed ID16845083