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 | |
| State | Published - Aug 12 2003 |
| Externally published | Yes |
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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 journal › Article
}
TY - JOUR
T1 - Serial BLAST searching
AU - Korf, Ian F
PY - 2003/8/12
Y1 - 2003/8/12
N2 - 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.
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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U2 - 10.1093/bioinformatics/btg199
DO - 10.1093/bioinformatics/btg199
M3 - Article
VL - 19
SP - 1492
EP - 1496
JO - Bioinformatics
JF - Bioinformatics
SN - 1367-4803
IS - 12
ER -