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Research and Development of High-performance Explosives
10:33

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Published on: February 20, 2016

A performance enhanced PSI-BLAST based on hybrid alignment.

Yuheng Li1, Nicholas Chia, Mario Lauria

  • 1Covidien, 60 Middletown Avenue, North Haven, CT 06473, USA.

Bioinformatics (Oxford, England)
|December 1, 2010
PubMed
Summary
This summary is machine-generated.

Hybrid PSI-BLAST improves homologous sequence detection by replacing deterministic alignments with a semi-probabilistic hybrid alignment. This enhances protein family modeling and identifies more distant homologs.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Sequence alignment is a fundamental tool in modern biology.
  • NCBI's PSI-BLAST uses iterative model building for sensitive detection of distant homologs.
  • PSI-BLAST's deterministic alignments limit its performance, especially for remote homologs.

Purpose of the Study:

  • To improve the sensitivity and performance of PSI-BLAST for detecting homologous sequences.
  • To integrate a semi-probabilistic alignment scheme into PSI-BLAST for enhanced model building.
  • To better identify remote homologous sequences.

Main Methods:

  • Replaced the Smith-Waterman alignment core in PSI-BLAST with a hybrid alignment algorithm.
  • Implemented position-specific gap penalties enabled by the hybrid algorithm's statistical properties.
  • Developed Hybrid PSI-BLAST for improved position-specific protein family modeling.

Main Results:

  • The new Hybrid PSI-BLAST demonstrates improved performance in identifying homologous sequences.
  • Position-specific gap penalties enhance the modeling of protein families.
  • The semi-probabilistic approach leads to more accurate detection of distant homologs.

Conclusions:

  • Hybrid PSI-BLAST offers superior performance over standard PSI-BLAST for sequence alignment.
  • The use of hybrid alignment and position-specific gap penalties advances protein family analysis.
  • This enhanced tool aids in the discovery of homologous sequences, particularly remote ones.