A space-efficient algorithm for local similarities - PubMed (original) (raw)
Comparative Study
A space-efficient algorithm for local similarities
X Q Huang et al. Comput Appl Biosci. 1990 Oct.
Abstract
Existing dynamic-programming algorithms for identifying similar regions of two sequences require time and space proportional to the product of the sequence lengths. Often this space requirement is more limiting than the time requirement. We describe a dynamic-programming local-similarity algorithm that needs only space proportional to the sum of the sequence lengths. The method can also find repeats within a single long sequence. To illustrate the algorithm's potential, we discuss comparison of a 73,360 nucleotide sequence containing the human beta-like globin gene cluster and a corresponding 44,594 nucleotide sequence for rabbit, a problem well beyond the capabilities of other dynamic-programming software.
Similar articles
- Dynamic programming algorithms for biological sequence comparison.
Pearson WR, Miller W. Pearson WR, et al. Methods Enzymol. 1992;210:575-601. doi: 10.1016/0076-6879(92)10029-d. Methods Enzymol. 1992. PMID: 1584052 - Recent developments in linear-space alignment methods: a survey.
Chao KM, Hardison RC, Miller W. Chao KM, et al. J Comput Biol. 1994 Winter;1(4):271-91. doi: 10.1089/cmb.1994.1.271. J Comput Biol. 1994. PMID: 8790471 - Locating well-conserved regions within a pairwise alignment.
Chao KM, Hardison RC, Miller W. Chao KM, et al. Comput Appl Biosci. 1993 Aug;9(4):387-96. doi: 10.1093/bioinformatics/9.4.387. Comput Appl Biosci. 1993. PMID: 8402204 - Finding homologs to nucleic acid or protein sequences using the framesearch program.
Healy M. Healy M. Curr Protoc Bioinformatics. 2002 Aug;Chapter 3:Unit 3.2. doi: 10.1002/0471250953.bi0302s00. Curr Protoc Bioinformatics. 2002. PMID: 18792937 Review. - Complete nucleotide sequence of the rabbit beta-like globin gene cluster: insights into evolution and regulation.
Hardison RC, Margot JB, Demers GW. Hardison RC, et al. Prog Clin Biol Res. 1989;316B:1-17. Prog Clin Biol Res. 1989. PMID: 2694173 Review.
Cited by
- A short note on dynamic programming in a band.
Gibrat JF. Gibrat JF. BMC Bioinformatics. 2018 Jun 15;19(1):226. doi: 10.1186/s12859-018-2228-9. BMC Bioinformatics. 2018. PMID: 29902968 Free PMC article. - Finding Protein and Nucleotide Similarities with FASTA.
Pearson WR. Pearson WR. Curr Protoc Bioinformatics. 2016 Mar 24;53:3.9.1-3.9.25. doi: 10.1002/0471250953.bi0309s53. Curr Protoc Bioinformatics. 2016. PMID: 27010337 Free PMC article. - Potential approaches for heterologous prion protein treatment of prion diseases.
Seelig DM, Goodman PA, Skinner PJ. Seelig DM, et al. Prion. 2016;10(1):18-24. doi: 10.1080/19336896.2015.1123372. Prion. 2016. PMID: 26636482 Free PMC article. - Profiling of human acquired immunity against the salivary proteins of Phlebotomus papatasi reveals clusters of differential immunoreactivity.
Geraci NS, Mukbel RM, Kemp MT, Wadsworth MN, Lesho E, Stayback GM, Champion MM, Bernard MA, Abo-Shehada M, Coutinho-Abreu IV, Ramalho-Ortigão M, Hanafi HA, Fawaz EY, El-Hossary SS, Wortmann G, Hoel DF, McDowell MA. Geraci NS, et al. Am J Trop Med Hyg. 2014 May;90(5):923-938. doi: 10.4269/ajtmh.13-0130. Epub 2014 Mar 10. Am J Trop Med Hyg. 2014. PMID: 24615125 Free PMC article. - Arginase and Arginine Decarboxylase - Where Do the Putative Gate Keepers of Polyamine Synthesis Reside in Rat Brain?
Peters D, Berger J, Langnaese K, Derst C, Madai VI, Krauss M, Fischer KD, Veh RW, Laube G. Peters D, et al. PLoS One. 2013 Jun 19;8(6):e66735. doi: 10.1371/journal.pone.0066735. Print 2013. PLoS One. 2013. PMID: 23840524 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Other Literature Sources