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Indexing Schemes for Similarity Search in Datasets of Short Protein Fragments by Aleksandar Stojmirović; Vladimir Pestov is a Computer Science article available to read on EtoBox.

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We propose a family of very efficient hierarchical indexing schemes for ungapped, score matrix-based similarity search in large datasets of short (4-12 amino acid) protein fragments. This type of similarity search has importance in both providing a building block to more complex algorithms and for possible use in direct biological investigations where datasets are of the order of 60 million objects. Our scheme is based on the internal geometry of the amino acid alphabet and performs exceptionally well, for example outputting 100 nearest neighbours to any possible fragment of length 10 after scanning on average less than 1% of the entire dataset.

Who reads Indexing Schemes for Similarity Search in Datasets of Short Protein Fragments?

Author

Aleksandar Stojmirović; Vladimir Pestov

Publisher

Elsevier Science; Elsevier ; Elsevier Science & Technology; Elsevier BV (ISSN 0959-2954)

Published

2007

Language

EN

Field

Computer Science (Physical Sciences)