Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms.

By William R. Pearson. 1991

Subfields: Computational Biology & Bioinformatics

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Citations in the corpus

GigaSpeech: An Evolving, Multi-domain ASR Corpus with 10, 000 Hours of Transcribed Audio (2021, methodology): “For each matched pair, hypothesis is further aligned with the transcript segment using the Smith-Waterman algorithm [13].”
BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences. (2016, methodology): “Internally, the GENES database is accompanied by the SSDB database, which contains amino acid sequence similarity scores and best-hit relations for all gene pairs in pairwise genome comparisons computed by the SSEARCH program [2].”
Use of Receiver Operating Characteristic (ROC) Analysis to Evaluate Sequence Matching (1996, methodology): “The sensitivity and specificity of sequence matching techniques are often evaluated by subjective methods (Pearson, 1991; Henikoff & Henikoff, 1992).”
SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications (2012, methodology): “its score is the same as (in which case the read mapping is not unique) or lower than (in which case the read mapping is unique) that of the optimal alignment. Although the latest version of SSEARCH (Pearson, 1991) can return detailed alignment corresponding to the optimal score, it is much slower t”
Advances in Protein Chemistry and Structural Biology (2010, methodology): “This comparison is carried out using the Smith–Waterman method as implemented in the FastA package (Pearson, 1991).”
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics (2003, methodology): “We used the Smith–Waterman algorithm as implemented in SSEARCH (Smith and Waterman 1981; Pearson 1991) to achieve a greater measure of sensitivity than BLASTP.”
Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors (2000, methodology): “Among the implementations of the Smith–Waterman algorithm, our implementation was found to be 13 times faster than OSEARCH and six times faster than SSEARCH.”
Estimating the tempo and mode of gene family evolution from comparative genomic data. (2005, methodology): “The two methods that we used to identify the offending branch agreed in every case”