Optimal alignments in linear space - PubMed (original) (raw)
Optimal alignments in linear space
E W Myers et al. Comput Appl Biosci. 1988 Mar.
Abstract
Space, not time, is often the limiting factor when computing optimal sequence alignments, and a number of recent papers in the biology literature have proposed space-saving strategies. However, a 1975 computer science paper by Hirschberg presented a method that is superior to the new proposals, both in theory and in practice. The goal of this paper is to give Hirschberg's idea the visibility it deserves by developing a linear-space version of Gotoh's algorithm, which accommodates affine gap penalties. A portable C-software package implementing this algorithm is available on the BIONET free of charge.
Similar articles
- Introducing variable gap penalties to sequence alignment in linear space.
Thompson JD. Thompson JD. Comput Appl Biosci. 1995 Apr;11(2):181-6. doi: 10.1093/bioinformatics/11.2.181. Comput Appl Biosci. 1995. PMID: 7620991 - Reduced space sequence alignment.
Grice JA, Hughey R, Speck D. Grice JA, et al. Comput Appl Biosci. 1997 Feb;13(1):45-53. doi: 10.1093/bioinformatics/13.1.45. Comput Appl Biosci. 1997. PMID: 9088708 - Local sequence alignments with monotonic gap penalties.
Mott R. Mott R. Bioinformatics. 1999 Jun;15(6):455-62. doi: 10.1093/bioinformatics/15.6.455. Bioinformatics. 1999. PMID: 10383814 - 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 - Sequence alignment and penalty choice. Review of concepts, case studies and implications.
Vingron M, Waterman MS. Vingron M, et al. J Mol Biol. 1994 Jan 7;235(1):1-12. doi: 10.1016/s0022-2836(05)80006-3. J Mol Biol. 1994. PMID: 8289235 Review.
Cited by
- Complete Genome Sequence of Enterotoxigenic Escherichia coli N4-Like Podophage Pollock.
Patel RS, Lessor LE, Hernandez AC, Kuty Everett GF. Patel RS, et al. Genome Announc. 2015 Jan 29;3(1):e01431-14. doi: 10.1128/genomeA.01431-14. Genome Announc. 2015. PMID: 25635029 Free PMC article. - Temporal patterns of bacterial communities in the Billings Reservoir system.
Marcondes MA, Pessôa R, José da Silva Duarte A, Clissa PB, Sanabani SS. Marcondes MA, et al. Sci Rep. 2024 Jan 24;14(1):2062. doi: 10.1038/s41598-024-52432-6. Sci Rep. 2024. PMID: 38267511 Free PMC article. - Alterations in immunized antigens of Anisakis pegreffii by ampicillin-induced gut microbiome changes in mice.
Kim M, Choi JH, Yi MH, Oh S, Yong TS, Kim JY. Kim M, et al. Parasites Hosts Dis. 2024 Aug;62(3):351-364. doi: 10.3347/PHD.23114. Epub 2024 Aug 26. Parasites Hosts Dis. 2024. PMID: 39218634 Free PMC article. - A tool for multiple sequence alignment.
Lipman DJ, Altschul SF, Kececioglu JD. Lipman DJ, et al. Proc Natl Acad Sci U S A. 1989 Jun;86(12):4412-5. doi: 10.1073/pnas.86.12.4412. Proc Natl Acad Sci U S A. 1989. PMID: 2734293 Free PMC article. - Cloning, genetic mapping, and expression analysis of an Arabidopsis thaliana gene that encodes 1-aminocyclopropane-1-carboxylate synthase.
Van der Straeten D, Rodrigues-Pousada RA, Villarroel R, Hanley S, Goodman HM, Van Montagu M. Van der Straeten D, et al. Proc Natl Acad Sci U S A. 1992 Oct 15;89(20):9969-73. doi: 10.1073/pnas.89.20.9969. Proc Natl Acad Sci U S A. 1992. PMID: 1357670 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Other Literature Sources
Miscellaneous