Nucleic Acids Research, 1988, Vol. 16, No. 22 10881-10890
© 1988
MOLECULAR BIOLOGY |
Multiple sequence alignment with hierarchical clustering
Laboratoire de Génétique Cellulaire, INRA Toulouse BP 27, 31326 Castanet Tolosan, France
Received July 7, 1988. Revised October 14, 1988. Accepted October 14, 1988.
An algorithm is presented for the multiple alignment of sequences, either proteins or nucleic acids, that is both accurate and easy to use on microcomputers. The approach is based on the conventional dynamic-programming method of pairwise alignment. Initially, a hierarchical clustering of the sequences is performed using the matrix of the pairwise alignment scores. The closest sequences are aligned creating groups of aligned sequences. Then close groups are aligned until all sequences are aligned in one group. The pairwise alignments included in the multiple alignment form a new matrix that is used to produce a hierarchical clustering. If it is different from the first one, iteration of the process can be performed. The method is illustrated by an example : a global alignment of 39 sequences of cytochrome c.
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R. Lefloch, J. Pouyssegur, and P. Lenormand Single and Combined Silencing of ERK1 and ERK2 Reveals Their Positive Contribution to Growth Signaling Depending on Their Expression Levels Mol. Cell. Biol., January 1, 2008; 28(1): 511 - 527. [Abstract] [Full Text] [PDF]
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L. Kotelawala, E. J. Grayhack, and E. M. Phizicky Identification of yeast tRNA Um44 2'-O-methyltransferase (Trm44) and demonstration of a Trm44 role in sustaining levels of specific tRNASer species RNA, January 1, 2008; 14(1): 158 - 169. [Abstract] [Full Text] [PDF]
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E. Chew, Y. Aweiss, C.-y. Lu, and F. Banuett Fuz1, a MYND domain protein, is required for cell morphogenesis in Ustilago maydis Mycologia, January 1, 2008; 100(1): 31 - 46. [Abstract] [Full Text] [PDF]
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B. Tawari, I. K. M. Ali, C. Scott, M. A. Quail, M. Berriman, N. Hall, and C. G. Clark Patterns of Evolution in the Unique tRNA Gene Arrays of the Genus Entamoeba Mol. Biol. Evol., January 1, 2008; 25(1): 187 - 198. [Abstract] [Full Text] [PDF]
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R. Muralla, E. Chen, C. Sweeney, J. A. Gray, A. Dickerman, B. J. Nikolau, and D. Meinke A Bifunctional Locus (BIO3-BIO1) Required for Biotin Biosynthesis in Arabidopsis Plant Physiology, January 1, 2008; 146(1): 60 - 73. [Abstract] [Full Text] [PDF]
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H. Eoh, A. C. Brown, L. Buetow, W. N. Hunter, T. Parish, D. Kaur, P. J. Brennan, and D. C. Crick Characterization of the Mycobacterium tuberculosis 4-Diphosphocytidyl-2-C-Methyl-D-Erythritol Synthase: Potential for Drug Development J. Bacteriol., December 15, 2007; 189(24): 8922 - 8927. [Abstract] [Full Text] [PDF]
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B. Cherif-Zahar, A. Durand, I. Schmidt, N. Hamdaoui, I. Matic, M. Merrick, and G. Matassi Evolution and Functional Characterization of the RH50 Gene from the Ammonia-Oxidizing Bacterium Nitrosomonas europaea J. Bacteriol., December 15, 2007; 189(24): 9090 - 9100. [Abstract] [Full Text] [PDF]
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A. Marrone, A. Walne, H. Tamary, Y. Masunari, M. Kirwan, R. Beswick, T. Vulliamy, and I. Dokal Telomerase reverse-transcriptase homozygous mutations in autosomal recessive dyskeratosis congenita and Hoyeraal-Hreidarsson syndrome Blood, December 15, 2007; 110(13): 4198 - 4205. [Abstract] [Full Text] [PDF]
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 C. Merlin, P. Lucas, D. Rochat, M.-C. Francois, M. Maibeche-Coisne, and E. Jacquin-Joly An Antennal Circadian Clock and Circadian Rhythms in Peripheral Pheromone Reception in the Moth Spodoptera littoralis J Biol Rhythms, December 1, 2007; 22(6): 502 - 514. [Abstract] [PDF]
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A. Macquet, M.-C. Ralet, O. Loudet, J. Kronenberger, G. Mouille, A. Marion-Poll, and H. M. North A Naturally Occurring Mutation in an Arabidopsis Accession Affects a {beta}-D-Galactosidase That Increases the Hydrophilic Potential of Rhamnogalacturonan I in Seed Mucilage PLANT CELL, December 1, 2007; 19(12): 3990 - 4006. [Abstract] [Full Text] [PDF]
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T. Lux, M. Nuhn, R. Hakenbeck, and P. Reichmann Diversity of Bacteriocins and Activity Spectrum in Streptococcus pneumoniae J. Bacteriol., November 1, 2007; 189(21): 7741 - 7751. [Abstract] [Full Text] [PDF]
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 J. M. Hillegass, C. M. Villano, K. R. Cooper, and L. A. White Matrix Metalloproteinase-13 Is Required for Zebra fish (Danio rerio) Development and Is a Target for Glucocorticoids Toxicol. Sci., November 1, 2007; 100(1): 168 - 179. [Abstract] [Full Text] [PDF]
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M. D. Allen, J. A. del Campo, J. Kropat, and S. S. Merchant FEA1, FEA2, and FRE1, Encoding Two Homologous Secreted Proteins and a Candidate Ferrireductase, Are Expressed Coordinately with FOX1 and FTR1 in Iron-Deficient Chlamydomonas reinhardtii Eukaryot. Cell, October 1, 2007; 6(10): 1841 - 1852. [Abstract] [Full Text] [PDF]
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C. Corratge, S. Zimmermann, R. Lambilliotte, C. Plassard, R. Marmeisse, J.-B. Thibaud, B. Lacombe, and H. Sentenac Molecular and Functional Characterization of a Na+-K+ Transporter from the Trk Family in the Ectomycorrhizal Fungus Hebeloma cylindrosporum J. Biol. Chem., September 7, 2007; 282(36): 26057 - 26066. [Abstract] [Full Text] [PDF]
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K. Abdelbaqi, A. Buissonniere, V. Prouzet-Mauleon, J. Gresser, I. Wesley, F. Megraud, and A. Menard Development of a Real-Time Fluorescence Resonance Energy Transfer PCR To Detect Arcobacter Species J. Clin. Microbiol., September 1, 2007; 45(9): 3015 - 3021. [Abstract] [Full Text] [PDF]
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R. Ioos, F. Panabieres, B. Industri, A. Andrieux, and P. Frey Distribution and Expression of Elicitin Genes in the Interspecific Hybrid Oomycete Phytophthora alni Appl. Envir. Microbiol., September 1, 2007; 73(17): 5587 - 5597. [Abstract] [Full Text] [PDF]
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 Y.-M. J. Lin, S.-C. Chao, T.-M. Chen, T.-J. Lai, J.-S. Chen, and H. S. Sun Association of Functional Polymorphisms of the Human Tryptophan Hydroxylase 2 Gene With Risk for Bipolar Disorder in Han Chinese Arch Gen Psychiatry, September 1, 2007; 64(9): 1015 - 1024. [Abstract] [Full Text] [PDF]
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N. Beerens, B. Selisko, S. Ricagno, I. Imbert, L. van der Zanden, E. J. Snijder, and B. Canard De Novo Initiation of RNA Synthesis by the Arterivirus RNA-Dependent RNA Polymerase J. Virol., August 15, 2007; 81(16): 8384 - 8395. [Abstract] [Full Text] [PDF]
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J. Breton, E. Bart-Delabesse, S. Biligui, A. Carbone, X. Seiller, M. Okome-Nkoumou, C. Nzamba, M. Kombila, I. Accoceberry, and M. Thellier New Highly Divergent rRNA Sequence among Biodiverse Genotypes of Enterocytozoon bieneusi Strains Isolated from Humans in Gabon and Cameroon J. Clin. Microbiol., August 1, 2007; 45(8): 2580 - 2589. [Abstract] [Full Text] [PDF]
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 G. Zabala and L. O. Vodkin A Rearrangement Resulting in Small Tandem Repeats in the F3'5'H Gene of White Flower Genotypes Is Associated with the Soybean W1 Locus Crop Sci., July 16, 2007; 47(S2): S-113 - S-124. [Abstract] [Full Text] [PDF]
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 M. F. Azpiroz and M. Lavina Modular Structure of Microcin H47 and Colicin V Antimicrob. Agents Chemother., July 1, 2007; 51(7): 2412 - 2419. [Abstract] [Full Text] [PDF]
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W. Fan, A. Idnurm, J. Breger, E. Mylonakis, and J. Heitman Eca1, a Sarcoplasmic/Endoplasmic Reticulum Ca2+-ATPase, Is Involved in Stress Tolerance and Virulence in Cryptococcus neoformans Infect. Immun., July 1, 2007; 75(7): 3394 - 3405. [Abstract] [Full Text] [PDF]
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M. Magnusson, R. Tobes, J. Sancho, and E. Pareja Cutting Edge: Natural DNA Repetitive Extragenic Sequences from Gram-Negative Pathogens Strongly Stimulate TLR9 J. Immunol., July 1, 2007; 179(1): 31 - 35. [Abstract] [Full Text] [PDF]
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