Reducing storage requirements for biological sequence comparison

• Published in: Bioinformatics Vol. 20; no. 18; pp. 3363 - 3369
• Main Authors: Roberts, Michael, Hayes, Wayne, Hunt, Brian R., Mount, Stephen M., Yorke, James A.
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 12.12.2004; Oxford Publishing Limited (England)
• Subjects: Algorithms; Biological and medical sciences; Databases, Genetic; Fundamental and applied biological sciences. Psychology; General aspects; Information Storage and Retrieval - methods; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Numerical Analysis, Computer-Assisted; Sequence Alignment - methods; Sequence Analysis - methods; Bioinformatics; Storage
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/bth408

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.