The genetic data environment an expandable GUI for multiple sequence analysis
Millipore BioImage, Ann Arbor, MI
1Mathematics and Computer Science Division, Argonne National Laboratory 9000 S. Cass Ave. Argonne, IL 60439
2Department of Microbiology, University of Illinois 407 S.Goodwin Ave. Urbana IL. 61801
3Harvard Genome Laboratory, Harvard University 16 Divinity Ave. Cambridge, MA 12138
4National Center for Human Genome Research, National Institutes of Health Bethesda, MD 20892 USA
5To whom reprint requests should be sent
An X-Windows-based graphic user interface is presented which allows the seamless integration of numerous existing biomolecular programs into a single analysis environment. This environment is based on a core multiple sequence editor that is linked to external programs by a user-expandable menu system and is supported on Sun and DEC work stations. There is no limitation to the number of external functions that can be linked to the interface. The length and number of sequences that can be handled are limited only by the size of virtual memory present on the workstation. The sequence data itself is used as the reference point from which analysis is done, and scalable graphic views are supported. It is suggested that future software development utilizing this expandable, user-defined menu system and the I/O linkage of external programs will allow biologists to easily integrate expertise from disparate fields into a single environment.
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|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
 G. Burger, D. Saint-Louis, M. W. Gray, and B. F. Lang Complete Sequence of the Mitochondrial DNA of the Red Alga Porphyra purpurea: Cyanobacterial Introns and Shared Ancestry of Red and Green Algae PLANT CELL, September 1, 1999; 11(9): 1675 - 1694. [Abstract] [Full Text]
|
|
|
|
|
|
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|
|
|
|
|
|
G. May, F. Shaw, H. Badrane, and X. Vekemans The signature of balancing selection: Fungal mating compatibility gene evolution PNAS, August 3, 1999; 96(16): 9172 - 9177. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. S. Gernandt and A. Liston Internal transcribed spacer region evolution in Larix and Pseudotsuga (Pinaceae) Am. J. Botany, May 1, 1999; 86(5): 711 - 723. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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|
|
|
|
|
|
C Argentini, V La Sorsa, R Bruni, E D'Ugo, R Giuseppetti, and M Rapicetta Hepadnavirus evolution and molecular strategy of adaptation in a new host J. Gen. Virol., March 1, 1999; 80(3): 617 - 626. [Abstract]
|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
J. P. Zehr, M. T. Mellon, and S. Zani New Nitrogen-Fixing Microorganisms Detected in Oligotrophic Oceans by Amplification of Nitrogenase (nifH) Genes Appl. Envir. Microbiol., September 1, 1998; 64(9): 3444 - 3450. [Abstract] [Full Text]
|
|
|
|
|
|
P. Cavaco-Silva, N. C. Taveira, L. Rosado, M. H. Lourenco, J. Moniz-Pereira, N. W. Douglas, R. S. Daniels, and M. O. Santos-Ferreira Virological and Molecular Demonstration of Human Immunodeficiency Virus Type 2 Vertical Transmission J. Virol., April 1, 1998; 72(4): 3418 - 3422. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. C. Bailey Jr., S. Fischer, J. Schug, J. Crabtree, M. Gibson, and G. C. Overton GAIA: Framework Annotation of Genomic Sequence Genome Res., March 1, 1998; 8(3): 234 - 250. [Abstract] [Full Text]
|
|
|
|
|
|
G. A. Helt, S. Lewis, A. E. Loraine, and G. M. Rubin BioViews: Java-Based Tools for Genomic Data Visualization Genome Res., March 1, 1998; 8(3): 291 - 305. [Abstract] [Full Text]
|
|
|
|
|
|
E. L. Delwart, J. I. Mullins, P. Gupta, G. H. Learn Jr., M. Holodniy, D. Katzenstein, B. D. Walker, and M. K. Singh Human Immunodeficiency Virus Type 1 Populations in Blood and Semen J. Virol., January 1, 1998; 72(1): 617 - 623. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Departure from Neutrality at the Mitochondrial NADH Dehydrogenase Subunit 2 Gene in Humans, but Not in Chimpanzees Genetics, January 1, 1998; 148(1): 409 - 422.
|
|
|
|
 |
|
 P. G. Board, M. Coggan, G. Chelvanayagam, S. Easteal, L. S. Jermiin, G. K. Schulte, D. E. Danley, L. R. Hoth, M. C. Griffor, A. V. Kamath, et al. Identification, Characterization, and Crystal Structure of the Omega Class Glutathione Transferases J. Biol. Chem., August 4, 2000; 275(32): 24798 - 24806. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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|
|
|
|
|
|
M. H. Lahoud, S. Ristevski, D. J. Venter, L. S. Jermiin, I. Bertoncello, S. Zavarsek, S. Hasthorpe, J. Drago, D. de Kretser, P. J. Hertzog, et al. Gene Targeting of Desrt, a Novel ARID Class DNA-Binding Protein, Causes Growth Retardation and Abnormal Development of Reproductive Organs Genome Res., August 1, 2001; 11(8): 1327 - 1334. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Song, V. Llaca, E. Linton, and J. Messing Sequence, Regulation, and Evolution of the Maize 22-kD alpha Zein Gene Family Genome Res., November 1, 2001; 11(11): 1817 - 1825. [Abstract] [Full Text] [PDF]
|
|