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Related Experiment Videos

The accuracy of several multiple sequence alignment programs for proteins.

Paulo A S Nuin1, Zhouzhi Wang, Elisabeth R M Tillier

  • 1Division of Cancer Genomics and Proteomics, Ontario Cancer Institute, University Health Network, 101 College St, M5G 1L7, Toronto, Ontario, Canada. pnuin@uhnres.utoronto.ca

BMC Bioinformatics
|October 26, 2006
PubMed
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Evaluating protein alignment programs is challenging due to unknown evolutionary histories. Simprot simulations revealed alignment accuracy depends on indel frequency, with Mafft (L-INS-i) and ProbCons showing superior performance.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Assessing protein sequence alignment program accuracy is difficult because true evolutionary histories are often unknown.
  • Existing benchmark datasets may not cover the full spectrum of evolutionary scenarios.

Purpose of the Study:

  • To evaluate the accuracy of nine popular protein alignment programs.
  • To compare program performance using simulated sequence data with known evolutionary histories.

Main Methods:

  • Utilized Simprot simulation software to generate over 30,000 protein sequence alignment sets with controlled evolutionary parameters.
  • Tested nine widely-used protein alignment programs against simulated data and BAliBASE benchmarks.
  • Analyzed the impact of insertion/deletion (indel) frequency and size on alignment accuracy.

Related Experiment Videos

Main Results:

  • Alignment accuracy was highly sensitive to the number of insertions and deletions, with indel size having a lesser impact.
  • Results from Simprot simulations were largely consistent with those obtained from BAliBASE benchmarks.
  • Mafft (L-INS-i) and ProbCons demonstrated the highest accuracy among the tested programs.

Conclusions:

  • Simprot enables more comprehensive alignment accuracy assessment by simulating diverse evolutionary histories.
  • Mafft (L-INS-i) and ProbCons are recommended for accurate protein sequence alignment, with Mafft offering faster execution.