Fast and sensitive multiple sequence alignments on a microcomputer
Department of Genetics, Trinity College Dublin 2, Ireland
*To whom correspondence should be addressed
A strategy is described for the rapid alignment of many long nucleic acid or protein sequences on a microcomputer. The program described can handle up to 100 sequences of 1200 residues each. The approach is based on progressively aligning sequences according to the branching order in an initial phylogenetic tree. The results obtained using the package appear to be as sensitive as those from any other available method.
Received on October 7, 1988; accepted on December 6, 1988
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R. D. Adam, Y. R. Ortega, R. H. Gilman, and C. R. Sterling Intervening Transcribed Spacer Region 1 Variability in Cyclospora cayetanensis J. Clin. Microbiol., June 1, 2000; 38(6): 2339 - 2343. [Abstract] [Full Text]
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S. Heiland, N. Radovanovic, M. Höfer, J. Winderickx, and H. Lichtenberg Multiple Hexose Transporters of Schizosaccharomyces pombe J. Bacteriol., April 15, 2000; 182(8): 2153 - 2162. [Abstract] [Full Text]
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S. T. Al Rashid, I. Dakuna, H. Louie, D. Ng, P. Vandamme, W. Johnson, and V. L. Chan Identification of Campylobacter jejuni, C. coli, C. lari, C. upsaliensis, Arcobacter butzleri, and A. butzleri-Like Species Based on the glyA Gene J. Clin. Microbiol., April 1, 2000; 38(4): 1488 - 1494. [Abstract] [Full Text]
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A. J. M. Vriesema, J. Dankert, and S. A. J. Zaat A Shift from Oral to Blood pH Is a Stimulus for Adaptive Gene Expression of Streptococcus gordonii CH1 and Induces Protection against Oxidative Stress and Enhanced Bacterial Growth by Expression of msrA Infect. Immun., March 1, 2000; 68(3): 1061 - 1068. [Abstract] [Full Text] [PDF]
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P. Arcari, L. Masullo, M. Masullo, F. Catanzano, and V. Bocchini A NAD(P)H Oxidase Isolated from the Archaeon Sulfolobus solfataricus Is Not Homologous with Another NADH Oxidase Present in the Same Microorganism. BIOCHEMICAL CHARACTERIZATION OF THE ENZYME AND CLONING OF THE ENCODING GENE J. Biol. Chem., January 14, 2000; 275(2): 895 - 900. [Abstract] [Full Text] [PDF]
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C. Lanave, S. Liuni, F. Licciulli, and M. Attimonelli Update of AMmtDB: a database of multi-aligned Metazoa mitochondrial DNA sequences Nucleic Acids Res., January 1, 2000; 28(1): 153 - 154. [Abstract] [Full Text] [PDF]
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P. Gonzalez and J. Labarère Phylogenetic relationships of Pleurotus species according to the sequence and secondary structure of the mitochondrial small-subunit rRNA V4, V6 and V9 domains Microbiology, January 1, 2000; 146(1): 209 - 221. [Abstract] [Full Text]
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M. Gasparian, M. Pusterla, B. Baldan, P. M. Downey, O. Rossetto, P. P. de Laureto, F. Filippini, M. Terzi, and F. L. Schiavo Identification and Characterization of an 18-Kilodalton, VAMP-Like Protein in Suspension-Cultured Carrot Cells Plant Physiology, January 1, 2000; 122(1): 25 - 34. [Abstract] [Full Text] [PDF]
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O. A. Okstad, M. Gominet, B. Purnelle, M. Rose, D. Lereclus, and A.-B. Kolsto Sequence analysis of three Bacillus cereus loci carrying PlcR-regulated genes encoding degradative enzymes and enterotoxin Microbiology, November 1, 1999; 145(11): 3129 - 3138. [Abstract] [Full Text] [PDF]
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 Y. T Konttinen, M. Ainola, H. Valleala, J. Ma, H. Ida, J. Mandelin, R. W Kinne, S. Santavirta, T. Sorsa, C. López-Otín, et al. Analysis of 16 different matrix metalloproteinases (MMP-1 to MMP-20) in the synovial membrane: different profiles in trauma and rheumatoid arthritis Ann Rheum Dis, November 1, 1999; 58(11): 691 - 697. [Abstract] [Full Text]
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 S. W. Wong, E. P. Bergquam, R. M. Swanson, F. W. Lee, S. M. Shiigi, N. A. Avery, J. W. Fanton, and M. K. Axthelm Induction of B Cell Hyperplasia in Simian Immunodeficiency Virus–infected Rhesus Macaques with the Simian Homologue of Kaposi's Sarcoma–associated Herpesvirus J. Exp. Med., September 20, 1999; 190(6): 827 - 840. [Abstract] [Full Text] [PDF]
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S. P. Sanghani, P. C. Sanghani, and R. G. Moran Identification of Three Key Active Site Residues in the C-terminal Domain of Human Recombinant Folylpoly-gamma -glutamate Synthetase by Site-directed Mutagenesis J. Biol. Chem., September 17, 1999; 274(38): 27018 - 27027. [Abstract] [Full Text] [PDF]
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J. K. Morona, R. Morona, and J. C. Paton Comparative Genetics of Capsular Polysaccharide Biosynthesis in Streptococcus pneumoniae Types Belonging to Serogroup 19 J. Bacteriol., September 1, 1999; 181(17): 5355 - 5364. [Abstract] [Full Text]
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J. Stavnezer, S. P. Bradley, N. Rousseau, T. Pearson, A. Shanmugam, D. J. Waite, P. R. Rogers, and A. L. Kenter Switch Recombination in a Transfected Plasmid Occurs Preferentially in a B Cell Line That Undergoes Switch Recombination of Its Chromosomal Ig Heavy Chain Genes J. Immunol., August 15, 1999; 163(4): 2028 - 2040. [Abstract] [Full Text] [PDF]
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A. Bauernfeind, I. Schneider, R. Jungwirth, H. Sahly, and U. Ullmann A Novel Type of AmpC beta -Lactamase, ACC-1, Produced by a Klebsiella pneumoniae Strain Causing Nosocomial Pneumonia Antimicrob. Agents Chemother., August 1, 1999; 43(8): 1924 - 1931. [Abstract] [Full Text]
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A. M. Blinkovsky, T. Byun, K. M. Brown, and E. J. Golightly Purification, Characterization, and Heterologous Expression in Fusarium venenatum of a Novel Serine Carboxypeptidase from Aspergillus oryzae Appl. Envir. Microbiol., August 1, 1999; 65(8): 3298 - 3303. [Abstract] [Full Text]
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J.-F. Valarcher, H. Bourhy, J. Gelfi, and F. Schelcher Evaluation of a Nested Reverse Transcription-PCR Assay Based on the Nucleoprotein Gene for Diagnosis of Spontaneous and Experimental Bovine Respiratory Syncytial Virus Infections J. Clin. Microbiol., June 1, 1999; 37(6): 1858 - 1862. [Abstract] [Full Text]
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J. S. Cannon, F. Hamzeh, S. Moore, J. Nicholas, and R. F. Ambinder Human Herpesvirus 8-Encoded Thymidine Kinase and Phosphotransferase Homologues Confer Sensitivity to Ganciclovir J. Virol., June 1, 1999; 73(6): 4786 - 4793. [Abstract] [Full Text]
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P. F. Zhang, X. Chen, D. W. Fu, J. B. Margolick, and G. V. Quinnan Jr. Primary Virus Envelope Cross-Reactivity of the Broadening Neutralizing Antibody Response during Early Chronic Human Immunodeficiency Virus Type 1 Infection J. Virol., June 1, 1999; 73(6): 5225 - 5230. [Abstract] [Full Text]
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K. Rudi and K. S. Jakobsen Complex Evolutionary Patterns of tRNAUAALeu Group I Introns in Cyanobacterial Radiation J. Bacteriol., June 1, 1999; 181(11): 3445 - 3451. [Abstract] [Full Text]
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T. Chun, K. Wang, F. A. Zuckermann, and H. R. Gaskins Molecular Cloning and Characterization of a Novel CD1 Gene from the Pig J. Immunol., June 1, 1999; 162(11): 6562 - 6571. [Abstract] [Full Text] [PDF]
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S.-H. Yun, M. L. Berbee, O. C. Yoder, and B. G. Turgeon Evolution of the fungal self-fertile reproductive life style from self-sterile ancestors PNAS, May 11, 1999; 96(10): 5592 - 5597. [Abstract] [Full Text] [PDF]
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K. W. Walker and R. A. Bradshaw Yeast Methionine Aminopeptidase I. ALTERATION OF SUBSTRATE SPECIFICITY BY SITE-DIRECTED MUTAGENESIS J. Biol. Chem., May 7, 1999; 274(19): 13403 - 13409. [Abstract] [Full Text] [PDF]
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S. Porwollik, B. Noonan, and P. W. O'Toole Molecular Characterization of a Flagellar Export Locus of Helicobacter pylori Infect. Immun., May 1, 1999; 67(5): 2060 - 2070. [Abstract] [Full Text] [PDF]
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C. Ros and S. Belák Studies of Genetic Relationships between Bovine, Caprine, Cervine, and Rangiferine Alphaherpesviruses and Improved Molecular Methods for Virus Detection and Identification J. Clin. Microbiol., May 1, 1999; 37(5): 1247 - 1253. [Abstract] [Full Text]
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E. S. Paterson, M. I. Moré, G. Pillay, C. Cellini, R. Woodgate, G. C. Walker, V. N. Iyer, and S. C. Winans Genetic Analysis of the Mobilization and Leading Regions of the IncN plasmids pKM101 and pCU1 J. Bacteriol., April 15, 1999; 181(8): 2572 - 2583. [Abstract] [Full Text]
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