Nucleic Acids Research, 1988, Vol. 16, No. 5 1829-1836
© 1988
Articles |
‘DNA Strider’: a ‘C’ program for the fast analysis of DNA and protein sequences on the Apple Macintosh family of computers
Service de Biochimie, Bâtiment 142, Département de Biologie, Centre d'Etudes Nucléaires de Saclay 91191 Gif-sur-Yvette Cedex, France
Received August 17, 1987. Revised November 15, 1987. Accepted November 15, 1987.
DNA Strider is a new integrated DNA and Protein sequence analysis program written with the C language for the Macintosh Plus, SE and II computers. It has been designed as an easy to learn and use program as well as a fast and efficient tool for the day-to-day sequence analysis work. The program consists of a multi-window sequence editor and of various DNA and Protein analysis functions. The editor may use 4 different types of sequences (DNA, degenerate DNA, RNA and one-letter coded protein) and can handle simultaneously 6 sequences of any type up to 32.5 kB each. Negative numbering of the bases is allowed for DNA sequences. All classical restriction and translation analysis functions are present and can be performed in any order on any open sequence or part of a sequence. The main feature of the program is that the same analysis function can be repeated several times on different sequences, thus generating multiple windows on the screen. Many graphic capabilities have been incorporated such as graphic restriction map, hydrophobicity profile and the CAI plot - codon adaptation index according to Sharp and Li (1). The restriction sites search uses a newly designed fast hexamer look-ahead algorithm. Typical runtime for the search of all sites with a library of 130 restriction endonucleases is 1 second per 10000 bases. The circular graphic restriction map of the pBR322 plasmid can be therefore computed from its sequence and displayed on the Macintosh Plus screen within 2 seconds and its multiline restriction map obtained in a scrolling window within 5 seconds.(*)
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A. Kasravi, M. F. Walter, S. Brand, J. M. Mason, and H. Biessmann Molecular Cloning and Tissue-Specific Expression of the mutator2 Gene (mu2) in Drosophila melanogaster Genetics, July 1, 1999; 152(3): 1025 - 1035. [Abstract] [Full Text]
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N. Vizcaino, A. Cloeckaert, M. S. Zygmunt, and L. Fernandez-Lago Molecular Characterization of a Brucella Species Large DNA Fragment Deleted in Brucella abortus Strains: Evidence for a Locus Involved in the Synthesis of a Polysaccharide Infect. Immun., June 1, 1999; 67(6): 2700 - 2712. [Abstract] [Full Text] [PDF]
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S. M. O'Malley, S. L. Mouton, D. A. Occhino, M. T. Deanda, J. R. Rashidi, K. L. Fuson, C. E. Rashidi, M. Y. Mora, S. M. Payne, and D. P. Henderson Comparison of the Heme Iron Utilization Systems of Pathogenic Vibrios J. Bacteriol., June 1, 1999; 181(11): 3594 - 3598. [Abstract] [Full Text]
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J. M. Quinn, S. S. Nakamoto, and S. Merchant Induction of Coproporphyrinogen Oxidase in Chlamydomonas Chloroplasts Occurs via Transcriptional Regulation of Cpx1 Mediated by Copper Response Elements and Increased Translation from a Copper Deficiency-specific Form of the Transcript J. Biol. Chem., May 14, 1999; 274(20): 14444 - 14454. [Abstract] [Full Text] [PDF]
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A. Stratmann, T. Mahmud, S. Lee, J. Distler, H. G. Floss, and W. Piepersberg The AcbC Protein from Actinoplanes Species Is a C7-cyclitol Synthase Related to 3-Dehydroquinate Synthases and Is Involved in the Biosynthesis of the alpha -Glucosidase Inhibitor Acarbose J. Biol. Chem., April 16, 1999; 274(16): 10889 - 10896. [Abstract] [Full Text] [PDF]
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P. Aneja and T. C. Charles Poly-3-Hydroxybutyrate Degradation in Rhizobium (Sinorhizobium) meliloti: Isolation and Characterization of a Gene Encoding 3-Hydroxybutyrate Dehydrogenase J. Bacteriol., February 1, 1999; 181(3): 849 - 857. [Abstract] [Full Text]
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B. N. Krath and B. Hove-Jensen Organellar and Cytosolic Localization of Four Phosphoribosyl Diphosphate Synthase Isozymes in Spinach Plant Physiology, February 1, 1999; 119(2): 497 - 506. [Abstract] [Full Text]
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S. A. Whitham, M. L. Yamamoto, and J. C. Carrington Selectable viruses and altered susceptibility mutants in Arabidopsis thaliana PNAS, January 19, 1999; 96(2): 772 - 777. [Abstract] [Full Text] [PDF]
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Z.-Q. Luo and S. K. Farrand Cloning and Characterization of a Tetracycline Resistance Determinant Present in Agrobacterium tumefaciens C58 J. Bacteriol., January 15, 1999; 181(2): 618 - 626. [Abstract] [Full Text]
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M. Ferrer, J. Tao, G. Iruin, M. Sanchez-Ayuso, J. Gonzalez-Rodriguez, R. Parrilla, and C. Gonzalez-Manchon Truncation of Glycoprotein (GP) IIIa (triangle 616-762) Prevents Complex Formation With GPIIb: Novel Mutation in Exon 11 of GPIIIa Associated With Thrombasthenia Blood, December 15, 1998; 92(12): 4712 - 4720. [Abstract] [Full Text] [PDF]
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P.-L. Li, D. M. Everhart, and S. K. Farrand Genetic and Sequence Analysis of the pTiC58 trb Locus, Encoding a Mating-Pair Formation System Related to Members of the Type IV Secretion Family J. Bacteriol., December 1, 1998; 180(23): 6164 - 6172. [Abstract] [Full Text]
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W. C. Roberts, B. A. Mullikin, R. Lathigra, and M. S. Hanson Molecular Analysis of Sequence Heterogeneity among Genes Encoding Decorin Binding Proteins A and B of Borrelia burgdorferi Sensu Lato Infect. Immun., November 1, 1998; 66(11): 5275 - 5285. [Abstract] [Full Text] [PDF]
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P. Oelkers, A. Behari, D. Cromley, J. T. Billheimer, and S. L. Sturley Characterization of Two Human Genes Encoding Acyl Coenzyme A:Cholesterol Acyltransferase-related Enzymes J. Biol. Chem., October 9, 1998; 273(41): 26765 - 26771. [Abstract] [Full Text] [PDF]
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S. D. Leidich, A. S. Ibrahim, Y. Fu, A. Koul, C. Jessup, J. Vitullo, W. Fonzi, F. Mirbod, S. Nakashima, Y. Nozawa, et al. Cloning and Disruption of caPLB1, a Phospholipase B Gene Involved in the Pathogenicity of Candida albicans J. Biol. Chem., October 2, 1998; 273(40): 26078 - 26086. [Abstract] [Full Text] [PDF]
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J.-y. Chen, Q. Wang, Z. Fu, S. Zhou, and W. A. Fonzi Tca1, the Retrotransposon-Like Element of Candida albicans, Is a Degenerate and Inactive Element J. Bacteriol., July 15, 1998; 180(14): 3657 - 3662. [Abstract] [Full Text]
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D. A. Wright and D. F. Voytas Potential Retroviruses in Plants: Tat1 Is Related to a Group of Arabidopsis thaliana Ty3/gypsy Retrotransposons That Encode Envelope-Like Proteins Genetics, June 1, 1998; 149(2): 703 - 715. [Abstract] [Full Text] [PDF]
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D. L. Smith, D. A. Starrett, and K. C. Gross A Gene Coding for Tomato Fruit beta -Galactosidase II Is Expressed during Fruit Ripening . Cloning, Characterization, and Expression Pattern Plant Physiology, June 1, 1998; 117(2): 417 - 423. [Abstract] [Full Text]
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D. A. Haake, C. Martinich, T. A. Summers, E. S. Shang, J. D. Pruetz, A. M. McCoy, M. K. Mazel, and C. A. Bolin Characterization of Leptospiral Outer Membrane Lipoprotein LipL36: Downregulation Associated with Late-Log-Phase Growth and Mammalian Infection Infect. Immun., April 1, 1998; 66(4): 1579 - 1587. [Abstract] [Full Text] [PDF]
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S. C. Clouthier, S. K. Collinson, A. P. White, P. A. Banser, and W. W. Kay tRNAArg (fimU) and Expression of SEF14 and SEF21 in Salmonella enteritidis J. Bacteriol., February 15, 1998; 180(4): 840 - 845. [Abstract] [Full Text]
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M. Misonne and P. Hoet Species-specific plasmid sequences for PCR identification of the three species of Borrelia burgdorferi sensu lato involved in Lyme disease [In Process Citation] J. Clin. Microbiol., January 1, 1998; 36(1): 269 - 272. [Abstract] [Full Text]
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P. A. Colussi, C. H. Taron, J. C. Mack, and P. Orlean Human and Saccharomyces cerevisiae dolichol phosphate mannose synthases represent two classes of the enzyme, but both function in Schizosaccharomyces pombe PNAS, July 22, 1997; 94(15): 7873 - 7878. [Abstract] [Full Text] [PDF]
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A. Nantel and R. S. Quatrano Characterization of Three Rice Basic/Leucine Zipper Factors, Including Two Inhibitors of EmBP-1 DNA Binding Activity J. Biol. Chem., December 6, 1996; 271(49): 31296 - 31305. [Abstract] [Full Text] [PDF]
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S. D. Leidich and P. Orlean Gpi1, a Saccharomyces cerevisiae Protein That Participates in the First Step in Glycosylphosphatidylinositol Anchor Synthesis J. Biol. Chem., November 1, 1996; 271(44): 27829 - 27837. [Abstract] [Full Text] [PDF]
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