Serial BLAST searching

Ian F Korf

doi:10.1093/bioinformatics/btg199

Serial BLAST searching

Ian F Korf

Research output: Contribution to journal › Article › peer-review

12 Scopus citations

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 language	English (US)
Pages (from-to)	1492-1496
Number of pages	5
Journal	Bioinformatics
Volume	19
Issue number	12
DOIs	https://doi.org/10.1093/bioinformatics/btg199
State	Published - Aug 12 2003
Externally published	Yes

ASJC Scopus subject areas

Clinical Biochemistry
Computer Science Applications
Computational Theory and Mathematics

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10.1093/bioinformatics/btg199

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title = "Serial BLAST searching",

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.",

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AB - 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.

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Serial BLAST searching

Abstract

ASJC Scopus subject areas

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