Reducing storage requirements for biological sequence comparison.

TitleReducing storage requirements for biological sequence comparison.
Publication TypeJournal Articles
Year of Publication2004
AuthorsRoberts M, Hayes W, Hunt BR, Mount SM, Yorke JA
Date Published2004 Dec 12
Keywordsalgorithms, Databases, Genetic, Information Storage and Retrieval, Numerical Analysis, Computer-Assisted, sequence alignment, Sequence Analysis

MOTIVATION: Comparison of nucleic acid and protein sequences is a fundamental tool of modern bioinformatics. A dominant method of such string matching is the 'seed-and-extend' approach, in which occurrences of short subsequences called 'seeds' are used to search for potentially longer matches in a large database of sequences. Each such potential match is then checked to see if it extends beyond the seed. To be effective, the seed-and-extend approach needs to catalogue seeds from virtually every substring in the database of search strings. Projects such as mammalian genome assemblies and large-scale protein matching, however, have such large sequence databases that the resulting list of seeds cannot be stored in RAM on a single computer. This significantly slows the matching process.

RESULTS: We present a simple and elegant method in which only a small fraction of seeds, called 'minimizers', needs to be stored. Using minimizers can speed up string-matching computations by a large factor while missing only a small fraction of the matches found using all seeds.

Alternate JournalBioinformatics
PubMed ID15256412
Grant List1R01HG0294501 / HG / NHGRI NIH HHS / United States