A greedy algorithm for aligning DNA sequences - PubMed (original) (raw)
A greedy algorithm for aligning DNA sequences
Z Zhang et al. J Comput Biol. 2000 Feb-Apr.
Abstract
For aligning DNA sequences that differ only by sequencing errors, or by equivalent errors from other sources, a greedy algorithm can be much faster than traditional dynamic programming approaches and yet produce an alignment that is guaranteed to be theoretically optimal. We introduce a new greedy alignment algorithm with particularly good performance and show that it computes the same alignment as does a certain dynamic programming algorithm, while executing over 10 times faster on appropriate data. An implementation of this algorithm is currently used in a program that assembles the UniGene database at the National Center for Biotechnology Information.
Similar articles
- Fast, optimal alignment of three sequences using linear gap costs.
Powell DR, Allison L, Dix TI. Powell DR, et al. J Theor Biol. 2000 Dec 7;207(3):325-36. doi: 10.1006/jtbi.2000.2177. J Theor Biol. 2000. PMID: 11082303 - Aligning a DNA sequence with a protein sequence.
Zhang Z, Pearson WR, Miller W. Zhang Z, et al. J Comput Biol. 1997 Fall;4(3):339-49. doi: 10.1089/cmb.1997.4.339. J Comput Biol. 1997. PMID: 9278064 - Winnowing sequences from a database search.
Berman P, Zhang Z, Wolf YI, Koonin EV, Miller W. Berman P, et al. J Comput Biol. 2000 Feb-Apr;7(1-2):293-302. doi: 10.1089/10665270050081531. J Comput Biol. 2000. PMID: 10890403 - sFFT: a faster accurate computation of the p-value of the entropy score.
Keich U. Keich U. J Comput Biol. 2005 May;12(4):416-30. doi: 10.1089/cmb.2005.12.416. J Comput Biol. 2005. PMID: 15882140 Review. - Pairwise sequence alignment--it's all about us!
Mullan L. Mullan L. Brief Bioinform. 2006 Mar;7(1):113-5. doi: 10.1093/bib/bbk008. Brief Bioinform. 2006. PMID: 16761368 Review. No abstract available.
Cited by
- Use of loop-mediated isothermal amplification for detection of Ophiostoma clavatum, the primary blue stain fungus associated with Ips acuminatus.
Villari C, Tomlinson JA, Battisti A, Boonham N, Capretti P, Faccoli M. Villari C, et al. Appl Environ Microbiol. 2013 Apr;79(8):2527-33. doi: 10.1128/AEM.03612-12. Epub 2013 Feb 8. Appl Environ Microbiol. 2013. PMID: 23396326 Free PMC article. - Identification of both copy number variation-type and constant-type core elements in a large segmental duplication region of the mouse genome.
Umemori J, Mori A, Ichiyanagi K, Uno T, Koide T. Umemori J, et al. BMC Genomics. 2013 Jul 8;14:455. doi: 10.1186/1471-2164-14-455. BMC Genomics. 2013. PMID: 23834397 Free PMC article. - Subtype analysis of Blastocystis isolates in Swedish patients.
Forsell J, Granlund M, Stensvold CR, Clark CG, Evengård B. Forsell J, et al. Eur J Clin Microbiol Infect Dis. 2012 Jul;31(7):1689-96. doi: 10.1007/s10096-011-1416-6. Epub 2012 Feb 15. Eur J Clin Microbiol Infect Dis. 2012. PMID: 22350386 - Genotype of a historic strain of Mycobacterium tuberculosis.
Bouwman AS, Kennedy SL, Müller R, Stephens RH, Holst M, Caffell AC, Roberts CA, Brown TA. Bouwman AS, et al. Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):18511-6. doi: 10.1073/pnas.1209444109. Epub 2012 Oct 22. Proc Natl Acad Sci U S A. 2012. PMID: 23091009 Free PMC article. - Exploration of multivariate analysis in microbial coding sequence modeling.
Mehmood T, Bohlin J, Kristoffersen AB, Sæbø S, Warringer J, Snipen L. Mehmood T, et al. BMC Bioinformatics. 2012 May 14;13:97. doi: 10.1186/1471-2105-13-97. BMC Bioinformatics. 2012. PMID: 22583558 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources