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A Practical Guide to Phylogenetics for Nonexperts
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Published on: February 5, 2014

Multithreaded multiple sequence alignments.

Joanne Bai1, Siamak Rezaei

  • 1Computer Science, UNBC, Canada. bai@unbc.ca.

Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference
|February 7, 2007
PubMed
Summary

Two multithreaded multiple sequence alignment methods were developed. Multiple-tree alignment showed better speedup, but both methods need improved sensitivity with increased threads.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Multiple sequence alignment (MSA) is crucial for understanding evolutionary relationships and protein function.
  • Existing MSA algorithms face challenges with scalability and sensitivity for large datasets.
  • Multithreaded approaches are explored to accelerate MSA computation.

Purpose of the Study:

  • To implement and evaluate two novel multithreaded multiple sequence alignment programs.
  • To assess the impact of guide tree application strategies on alignment speed and sensitivity.
  • To identify potential areas for improving the performance of parallel MSA algorithms.

Main Methods:

  • Development of two multithreaded MSA programs based on progressive alignment and divide-and-conquer strategies.
  • Single-tree alignment: Utilizes a single guide tree for all sub-alignments.
  • Multiple-tree alignment: Employs individual guide trees for aligned sequence fragments.

Main Results:

  • Multiple-tree alignment demonstrated superior speedup performance compared to single-tree alignment.
  • Neither alignment strategy achieved ideal sensitivity results as the number of threads increased.
  • Performance bottlenecks were observed with increasing computational parallelism.

Conclusions:

  • Multithreaded MSA approaches offer speed improvements, particularly with the multiple-tree strategy.
  • Further optimization is required to enhance alignment sensitivity in parallel environments.
  • Heuristic methods like overlapping and sliding window alignments are proposed for future improvements.