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.