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Related Experiment Videos

Fast and sensitive multiple alignment of large genomic sequences.

Michael Brudno1, Michael Chapman, Berthold Göttgens

  • 1Department of Computer Science, Stanford University, Stanford, CA 94305, USA. brudno@cs.stanford.edu

BMC Bioinformatics
|December 25, 2003
PubMed
Summary
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The CHAOS algorithm rapidly identifies sequence similarities, enhancing DIALIGN for faster, sensitive multiple genome alignments. This combination accurately identifies functional genomic elements like genes and regulatory sequences.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Genomic sequence alignment is crucial for analyzing and annotating genomes, identifying functional sites like genes and regulatory elements.
  • Multiple sequence alignment plays an increasingly vital role in genome studies due to the growing number of sequenced genomes.
  • Existing alignment tools often trade speed for sensitivity, necessitating novel approaches.

Purpose of the Study:

  • To develop a novel algorithm for the rapid identification of local pair-wise sequence similarities.
  • To integrate this algorithm with a sensitive multiple alignment tool to improve efficiency without compromising accuracy.
  • To demonstrate the utility of the combined approach in identifying functional genomic elements.

Main Methods:

Related Experiment Videos

  • The CHAOS algorithm was developed to quickly find chains of local sequence similarities.
  • Local alignments identified by CHAOS were used as anchor points for the DIALIGN multiple alignment tool.
  • The performance and accuracy of the DIALIGN/CHAOS combination were evaluated on genomic sequences.

    • Main Results:

    • CHAOS enables the rapid identification of local sequence similarities, serving as effective anchor points.
    • The DIALIGN/CHAOS combination reduced DIALIGN's running time by over 95% for large genomic sequences.
    • The approach accurately identified exons and regulatory elements in genomic sequences around the stem-cell-leukemia (SCL) gene.

    Conclusions:

    • The CHAOS local alignment tool significantly accelerates global alignment tools like DIALIGN without sacrificing alignment quality.
    • The DIALIGN/CHAOS combination demonstrates effectiveness in accurately aligning short regulatory sequences across distant orthologous genes.
    • This approach offers a powerful method for efficient and sensitive genome analysis and annotation.