Optimal alignments in linear space
1Department of Computer Science, University of Arizona Tucson, AZ 85721, USA
2Department of Computer Science, The Pennsylvania State University University Park, PA 16802, USA
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.
Received on October 14, 1987; accepted on December 19, 1987
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C. Feschotte and C. Mouches Evidence that a Family of Miniature Inverted-Repeat Transposable Elements (MITEs) from the Arabidopsis thaliana Genome Has Arisen from a pogo-like DNA Transposon Mol. Biol. Evol., May 1, 2000; 17(5): 730 - 737. [Abstract] [Full Text] [PDF]
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 L. R. Murphy, A. Wallqvist, and R. M. Levy Simplified amino acid alphabets for protein fold recognition and implications for folding Protein Eng. Des. Sel., March 1, 2000; 13(3): 149 - 152. [Abstract] [Full Text] [PDF]
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D. O. V. Alonso and V. Daggett Staphylococcal protein A: Unfolding pathways, unfolded states, and differences between the B and E domains PNAS, January 4, 2000; 97(1): 133 - 138. [Abstract] [Full Text] [PDF]
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A. R. Caballero, R. Lottenberg, and K. H. Johnston Cloning, Expression, Sequence Analysis, and Characterization of Streptokinases Secreted by Porcine and Equine Isolates of Streptococcus equisimilis Infect. Immun., December 1, 1999; 67(12): 6478 - 6486. [Abstract] [Full Text] [PDF]
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P. S. Beisser, G. Grauls, C. A. Bruggeman, and C. Vink Deletion of the R78 G Protein-Coupled Receptor Gene from Rat Cytomegalovirus Results in an Attenuated, Syncytium-Inducing Mutant Strain J. Virol., September 1, 1999; 73(9): 7218 - 7230. [Abstract] [Full Text]
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X. Huang and A. Madan CAP3: A DNA Sequence Assembly Program Genome Res., September 1, 1999; 9(9): 868 - 877. [Abstract] [Full Text]
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 E. Danty, L. Briand, C. Michard-Vanhee, V. Perez, G. Arnold, O. Gaudemer, D. Huet, J.-C. Huet, C. Ouali, C. Masson, et al. Cloning and Expression of a Queen Pheromone-Binding Protein in the Honeybee: an Olfactory-Specific, Developmentally Regulated Protein J. Neurosci., September 1, 1999; 19(17): 7468 - 7475. [Abstract] [Full Text] [PDF]
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F. Dzierszinski, O. Popescu, C. Toursel, C. Slomianny, B. Yahiaoui, and S. Tomavo The Protozoan Parasite Toxoplasma gondii Expresses Two Functional Plant-like Glycolytic Enzymes. IMPLICATIONS FOR EVOLUTIONARY ORIGIN OF APICOMPLEXANS J. Biol. Chem., August 27, 1999; 274(35): 24888 - 24895. [Abstract] [Full Text] [PDF]
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C. A. Collins and C. Guthrie Allele-specific genetic interactions between Prp8 and RNA active site residues suggest a function for Prp8 at the catalytic core of the spliceosome Genes & Dev., August 1, 1999; 13(15): 1970 - 1982. [Abstract] [Full Text]
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F. R. Sallmann, S. Baveye-Descamps, F. Pattus, V. Salmon, N. Branza, G. Spik, and D. Legrand Porins OmpC and PhoE of Escherichia coli as Specific Cell-surface Targets of Human Lactoferrin. BINDING CHARACTERISTICS AND BIOLOGICAL EFFECTS J. Biol. Chem., June 4, 1999; 274(23): 16107 - 16114. [Abstract] [Full Text] [PDF]
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S. Hallin and P.-E. Lindgren PCR Detection of Genes Encoding Nitrite Reductase in Denitrifying Bacteria Appl. Envir. Microbiol., April 1, 1999; 65(4): 1652 - 1657. [Abstract] [Full Text]
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P. Gao, S. Watanabe, T. Ito, H. Goto, K. Wells, M. McGregor, A. J. Cooley, and Y. Kawaoka Biological Heterogeneity, Including Systemic Replication in Mice, of H5N1 Influenza A Virus Isolates from Humans in Hong Kong J. Virol., April 1, 1999; 73(4): 3184 - 3189. [Abstract] [Full Text]
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T. H. Grayson, L. F. Cooper, F. A. Atienzar, M. R. Knowles, and M. L. Gilpin Molecular Differentiation of Renibacterium salmoninarum Isolates from Worldwide Locations Appl. Envir. Microbiol., March 1, 1999; 65(3): 961 - 968. [Abstract] [Full Text]
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K. de Fays, A. Tibor, C. Lambert, C. Vinals, P. Denoel, X. De Bolle, J. Wouters, J.-J. Letesson, and E. Depiereux Structure and function prediction of the Brucella abortus P39 protein by comparative modeling with marginal sequence similarities Protein Eng. Des. Sel., March 1, 1999; 12(3): 217 - 223. [Abstract] [Full Text] [PDF]
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V. G. H. Eijsink, M. Skeie, P. H. Middelhoven, M. B. Brurberg, and I. F. Nes Comparative Studies of Class IIa Bacteriocins of Lactic Acid Bacteria Appl. Envir. Microbiol., September 1, 1998; 64(9): 3275 - 3281. [Abstract] [Full Text]
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C. Bauerle, C. Magembe, and D. P. Briskin Characterization of a Red Beet Protein Homologous to the Essential 36-Kilodalton Subunit of the Yeast V-Type ATPase Plant Physiology, July 1, 1998; 117(3): 859 - 867. [Abstract] [Full Text] [PDF]
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M. Nilsson, L. Frykberg, J.-I. Flock, L. Pei, M. Lindberg, and B. Guss A Fibrinogen-Binding Protein of Staphylococcus epidermidis Infect. Immun., June 1, 1998; 66(6): 2666 - 2673. [Abstract] [Full Text] [PDF]
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A. R. Mushegian, J. R. Garey, J. Martin, and L. X. Liu Large-Scale Taxonomic Profiling of Eukaryotic Model Organisms: A Comparison of Orthologous Proteins Encoded by the Human, Fly, Nematode, and Yeast Genomes Genome Res., June 1, 1998; 8(6): 590 - 598. [Abstract] [Full Text]
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 M. De las Alas, R. A. M. de bruin, L. T. Eyck, G. Los, and S. B. Howell Prediction-based threading of the hMSH2 DNA mismatch repair protein FASEB J, June 1, 1998; 12(9): 653 - 663. [Abstract] [Full Text]
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