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Comparison of Current BLAST Software on Nucleotide Sequences.

I Elizabeth Cha1, Eric C Rouchka

  • 1University of Louisville Department of Computer Engineering and Computer Science, Louisville, KY 40292, icha@louisville.edu.

Proceedings. IPDPS (Conference)
|September 28, 2011
PubMed
Summary
This summary is machine-generated.

BLAST (Basic Local Alignment Search Tool) implementations show varying efficiencies for searching large genomic databases. WU BLAST is best for unknown compositions, NCBI BLAST for small databases, and mpiBLAST excels with large distributed databases.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Exponential growth of biological sequence databases like GenBank necessitates efficient search tools.
  • The Basic Local Alignment Search Tool (BLAST) is a widely used algorithm for sequence alignment.
  • Evaluating different BLAST implementations is crucial for optimizing computational resource allocation.

Purpose of the Study:

  • To compare the efficiency of three BLAST implementations (WU BLAST, NCBI BLAST, mpiBLAST) for nucleotide-nucleotide comparisons.
  • To assess performance across diverse database sizes and query characteristics using human genomic and EST sequences.
  • To identify optimal usage scenarios for each BLAST implementation based on database and query properties.

Main Methods:

  • Performance evaluation of WU BLAST, NCBI BLAST, and mpiBLAST.
  • Utilizing target databases and query sequences of varying lengths and entry counts.
  • Constructing test datasets from human genomic and expressed sequence tag (EST) data.

Main Results:

  • WU BLAST demonstrated superior efficiency when database and query compositions were unknown.
  • NCBI BLAST performed optimally with smaller databases containing fewer sequences.
  • mpiBLAST highlighted the advantages of database distribution for large-scale genomic datasets.
  • The optimal number of compute nodes for mpiBLAST was found to be relatively low across tested scenarios.

Conclusions:

  • The choice of BLAST implementation significantly impacts search efficiency in large-scale genomic analyses.
  • WU BLAST offers general efficiency, NCBI BLAST is suitable for smaller datasets, and mpiBLAST is powerful for distributed, large databases.
  • Understanding these performance characteristics aids in selecting the most effective tool for specific bioinformatics tasks and resource constraints.