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Simple adjustment of the sequence weight algorithm remarkably enhances PSI-BLAST performance.

Toshiyuki Oda1, Kyungtaek Lim2, Kentaro Tomii3,4

  • 1Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan. laevis@xenopus.sakura.ne.jp.

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Summary
This summary is machine-generated.

Modifying Position-Specific Iterated Basic Local Alignment Search Tool (PSI-BLAST) to prevent narrow blocks significantly improves its performance in sequence similarity searches. The enhanced PSI-BLASTexB tool consistently outperforms the original PSI-BLAST.

Keywords:
PSI-BLASTPosition-specific scoring matrixSequence similarity searchSequence weighting

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Position-Specific Iterated Basic Local Alignment Search Tool (PSI-BLAST) is a popular tool for sequence similarity searches.
  • It utilizes Position-Specific Scoring Matrices (PSSMs) derived from multiple sequence alignments (MSAs) for enhanced homolog detection.
  • Accurate sequence weighting within MSAs is critical for PSSM construction, with PSI-BLAST dividing MSAs into blocks for this purpose.

Purpose of the Study:

  • To investigate the impact of narrow block widths on PSI-BLAST performance.
  • To develop an improved version of PSI-BLAST that addresses limitations caused by narrow block calculations.
  • To evaluate the performance enhancement of the modified tool.

Main Methods:

  • Analyzing the block width distribution in standard PSI-BLAST to identify narrow blocks.
  • Modifying the PSI-BLAST algorithm to enforce a minimum block width (MBW).
  • Comparing the performance of the modified PSI-BLAST (PSI-BLASTexB) against the original PSI-BLAST using benchmark datasets.

Main Results:

  • PSI-BLAST frequently generates blocks with widths less than 5, negatively impacting its performance.
  • The modified PSI-BLAST, PSI-BLASTexB, with an MBW of 25, consistently outperforms the original PSI-BLAST across three benchmark sets.
  • Performance gains are more pronounced when using MSAs as queries compared to single sequences.

Conclusions:

  • Narrow block generation is a key factor limiting PSI-BLAST's search performance.
  • Enforcing a minimum block width in PSI-BLASTexB significantly enhances its performance.
  • PSI-BLASTexB offers improved sequence similarity search capabilities, with source code available.