Reducing storage requirements for biological sequence comparison

M. Roberts, W. Hayes, B. R. Hunt, S. M. Mount, J. A. Yorke
2004 Bioinformatics  
Motivation: Comparison of nucleic acid and protein sequences is a fundamental tool of modern bioinformatics. A dominant method of such string matching is the 'seedand-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
more » ... om 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.
doi:10.1093/bioinformatics/bth408 pmid:15256412 fatcat:i7c3job55jdw3g4dyyzkq6t2rm