title: AliWABA: alignment on the web through an A-Bruijn approach.
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.
  
  
  BACKGROUND
  http://aba.nbcr.net/
authors.affiliation: Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA. ncjones@cs.uscd.edu
authors.forename: Neil C
authors.initials: NC
authors.lastname: Jones
authors.forename: Degui
authors.initials: D
authors.lastname: Zhi
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Raphael
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001483:Base Sequence; D003196:Computer Graphics; D020407:Internet; D050809:POU Domain Factors / Q000737:chemistry; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D050809:POU Domain Factors