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

Neil C Jones1, Degui Zhi, Benjamin J Raphael

  • 1Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA. ncjones@cs.uscd.edu

Nucleic Acids Research
|July 18, 2006
PubMed
Summary

A-Bruijn Alignment (ABA) simplifies sequence alignment using graph representations. The AliWABA web server aids in analyzing repeated and shuffled subsequences, particularly for protein domain analysis.

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Area of Science:

  • Computational Biology
  • Bioinformatics

Background:

  • Multiple sequence alignment is crucial in computational biology.
  • A-Bruijn Alignment (ABA) uses directed graphs for sequence alignment.
  • ABA is effective for sequences with repeated or shuffled subsequences.

Purpose of the Study:

  • Introduce AliWABA, a web server for ABA alignments.
  • Simplify the analysis of local similarities in reordered sequences.
  • Facilitate protein domain analysis by integrating with the Conserved Domain Database.

Main Methods:

  • Utilizes the A-Bruijn Alignment (ABA) method.
  • Represents sequence alignments as directed graphs.
  • Provides tools for alignment generation, graph visualization, and subsequence extraction.

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Main Results:

  • AliWABA simplifies the analysis of complex sequence similarities.
  • Enables efficient handling of repeated and shuffled subsequences.
  • Offers direct querying of the Conserved Domain Database for protein domain analysis.

Conclusions:

  • AliWABA is a valuable tool for computational biologists.
  • The web server enhances the analysis of sequence alignments, especially for protein domains.
  • Facilitates discovery of local similarities in reordered biological sequences.