Homology search with binary and trinary scoring matrices

Protein homology search can be accelerated with the use of bit-parallel algorithms in conjunction with constraints on the values contained in the scoring matrices. Trinary scoring matrices (containing only the values -1, 0, and 1) allow for significant acceleration without significant reduction in t...

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Vydáno v:International journal of bioinformatics research and applications Ročník 2; číslo 2; s. 119
Hlavní autor: Smith, Scott F
Médium: Journal Article
Jazyk:angličtina
Vydáno: Switzerland 2006
Témata:
Algorithms
Computational Biology - methods
Databases, Protein
False Positive Reactions
Models, Statistical
Proteins - chemistry
ROC Curve
Sensitivity and Specificity
Sequence Alignment
Sequence Analysis
Sequence Analysis, Protein
Software
ISSN:1744-5485
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Shrnutí:Protein homology search can be accelerated with the use of bit-parallel algorithms in conjunction with constraints on the values contained in the scoring matrices. Trinary scoring matrices (containing only the values -1, 0, and 1) allow for significant acceleration without significant reduction in the receiver operating characteristic (ROC) score of a Smith-Waterman search. Binary scoring matrices (containing the values 0 and 1) result in some reduction in ROC score, but result in even more acceleration. Binary scoring matrices and five-bit saturating scores can be used for fast prefilters to the Smith-Waterman algorithm.
Bibliografie:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:1744-5485
DOI:10.1504/IJBRA.2006.009763