Serial BLAST searching

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

Motivation: The translating BLAST algorithms are powerful tools for finding protein-coding genes because they identify amino acid similarities in nucleotide sequences. Unfortunately, these kinds of searches are computationally intensive and often represent bottlenecks in sequence analysis pipelines. Tuning parameters for speed can make the searches much faster, but one risks losing low-scoring alignments. However, high scoring alignments are relatively resistant to such changes in parameters, and this fact makes it possible to use a serial strategy where a fast, insensitive search is used to pre-screen a database for similar sequences, and a slow, sensitive search is used to produce the sequence alignments. Results: Serial BLAST searches improve both the speed and sensitivity.

Original languageEnglish (US)
Pages (from-to)1492-1496
Number of pages5
JournalBioinformatics
Volume19
Issue number12
DOIs
StatePublished - Aug 12 2003
Externally publishedYes

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Sequence Alignment
Sequence Analysis
Databases
Amino Acids
Proteins
Scoring
Nucleotides
Alignment
Amino acids
Tuning
Pipelines
Genes
Parameter Tuning
Coding
Gene
Protein

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

Cite this

Serial BLAST searching. / Korf, Ian F.

In: Bioinformatics, Vol. 19, No. 12, 12.08.2003, p. 1492-1496.

Research output: Contribution to journalArticle

Korf, Ian F. / Serial BLAST searching. In: Bioinformatics. 2003 ; Vol. 19, No. 12. pp. 1492-1496.
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