GeneMark Manual

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Resources and References


More information about Gene Probe, Inc and GeneMark can be found on our WWW page at .

You can also find valuable information about GeneMark at the Georgia Institute of Technology at .

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This software package should be referenced as:

GeneMark v. 2.4, Gene Probe, Inc.

The primary reference for the GeneMark program is:

Borodovsky, M., and McIninch, J. D. (1993) "GeneMark: Parallel gene recognition for both DNA strands," Comp. Chem., 17, pp. 123-133

Other GeneMark related articles

Hayes, W. S. and Borodovsky, M. (1998) "How to interpret an anonymous genome? Learning Markov models for gene identification in parallel with the sequence annotation," Genome Research

Hayes, W. S., and Borodovsky, M. (1998) "Deriving Ribosomal Binding Site (RBS) statistical models from unannotated DNA sequences and the use of the RBS model for N-terminal prediction," accepted for the Proceedings of Third Pacific Symposium on Biocomputing (PSB '98)

Tomb, J. F. et al. (1997) "The complete genome sequence of the gastric pathogen Helicobacter pylori," Nature, 388, pp. 539-547

Benian, G., Tinley, T. L., Tang, X. and Borodovsky, M. (1996) "The C. elegans Gene unc-89, Required for Muscle M-line Assembly, Encodes a Giant Modular Protein Composed of Ig and Signal Transduction Domains," Journal of Cell Biology, 6, pp. 835-848

Kleffe, J., Hermann, K., and Borodovsky, M. (1996) "Statistical Analysis of GeneMark Performance by Cross-validation," Computers & Chemistry, 20, pp. 123-134

Tatusov, R.L., Mushegian, A.R., Bork, P., Brown, N.P.,Hayes, W.S., Borodovsky, M., Rudd, K.E. and Koonin, E.V. (1996) "Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli. Current Biology, 6, pp. 279-291.

McIninch, J. D., Hayes, W. S., and Borodovsky, M. (1996) "Applications of GeneMark in Multispecies Environments," in the Proceedings of the Fourth Internation Conference on Intelligent Systems for Molecular Biology (ISMB96), June 12-15, 1996. AAAI Press, Menlo Park, CA. pp. 165-175

Hirosawa, M., Kaneko, T., Tabata, S., McIninch, J. D., Hayes, W., Borodovsky, M., Isono, K. (1995) "Prediction of the Coding Regions in a Contiguous 1MB Sequence of the Genome of Synechocystis sp. Strain PCC6803" DNA Research, 2, pp. 239-246

Borodovsky, M., McIninch, J. D., Koonin, E. V., Rudd, K. E., M├ędigue, C., and Danchin, A. (1995) "Detection of new genes in a bacterial genome using Markov models for three gene classes," Nucl. Acids Res., 23, pp. 3554-3562

Borodovsky, M., McIninch, J. D., Hayes, W. (1995) "Gene Identification in Genomic DNA by GeneMark and Similarity Search Methods." Genome Science and Technology, 1, p. 71

Borodovsky, M., Koonin, E. V., and Rudd, K. E. (1994) "New genes in old sequence: a strategy for finding genes in the bacterial genome," TIBS, 19, pp. 309-313

Borodovsky, M., Koonin, E. V., and Rudd, K. E. (1994) "Intrinsic and extrinsic approaches for detecting genes in a bacterial genome, " Nucl. Acids Res., 22, pp. 4756-4767

Borodovsky, M., and McIninch, J. D. (1993) "Recognition of genes in DNA sequence with ambiguities, " BioSystems, 30, pp. 161-171

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