Improved sensitivity of biological sequence database searches

We have increased the sensitivity ofDNA and protein sequence database searches by allowing similar but non-identical amino acids or nucleotides to match. In addition, one can match k-tuples or words instead of matching individual residues in order to speed the search. A matching matrix specifies whi...

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Bibliographic Details
Published in:Bioinformatics 1990-07, Vol.6 (3), p.237-245
Main Authors: Brutlag, Douglas L., Dautricourt, Jean-Pierre, Maulik, Sunil, Relnh, John
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Base Sequence
Biological and medical sciences
Databases, Factual
Diverse techniques
Fundamental and applied biological sciences. Psychology
Mathematical Computing
Molecular and cellular biology
Software
User-Computer Interface
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Summary:We have increased the sensitivity ofDNA and protein sequence database searches by allowing similar but non-identical amino acids or nucleotides to match. In addition, one can match k-tuples or words instead of matching individual residues in order to speed the search. A matching matrix specifies which k-tuples match each other. The matching matrix can be calculated from a similarity matrix of amino acids and a threshold of similarity required for matching. This permits amino acid similarity matrices or replacement matrices (PAM matrices) to be used in the first step of a sequence comparison rather than in a secondary scoring phase. The concept of matching non-identical k-tuples also increases the power ofDNA database searches. For example, a matrix that specifies that any 3-tuple in a DNA sequence can match any other 3-tuple encoding the same amino acid permits a DNA database search using a DNA query sequence for regions that would encode a similar amino acid sequence.
ISSN:1367-4803
0266-7061
1460-2059
DOI:10.1093/bioinformatics/6.3.237