Data processing: artificial intelligence – Machine learning – Genetic algorithm and genetic programming system
Reexamination Certificate
2004-05-28
2009-11-03
Smith, Carolyn L. (Department: 1631)
Data processing: artificial intelligence
Machine learning
Genetic algorithm and genetic programming system
C702S019000, C703S002000, C706S011000, C707S793000
Reexamination Certificate
active
07613662
ABSTRACT:
A method and system for determining whether a sequence fragment g is atypical with respect to a reference sequence G using compositional methods and including constructing a template from G and g respectively containing a sequence of characters for a comparison with one another, wherein a number of characters contained in the template exceeds two. For the case where the sequences at hand are genetic, the atypicality detection can be used to determine whether a given sequence fragment g is the result of a horizontal transfer event.
REFERENCES:
patent: 2003/0224380 (2003-12-01), Becker et al.
Samuel Karlin, Allan M. Campbell, and Jan Mrazek, “Comparative DNA Analysis Across Diverse Genomes,”1998, Annu. Rev. Genet., vol. 32, pp. 185-225.
Toshimichi Ikemura, “Codon Usage and tRNA Content in Unicellular and Multicellular Organisms,”1985, Mol. Biol. Evol., vol. 2, No. 1, pp. 13-34.
Mark A. Ragan and Robert L. Charlebois, “Distributional profiles of homologous open reading frames among bacterial phyla: implications for vertical and lateral transmission,”2002, International Journal of Systematic and Evolutionary Microbiology, vol. 52, pp. 777-787.
Samuel Karlin, Jan Mrazek, and Allan M. Campbell, “Codon usages in different gene classes of theEscherichia coligenome,”1998, Molecular Microbiology, vol. 29, No. 6, pp. 1341-1355.
Samuel Karlin and Jan Mrazek, “What Drives Codon Choices in Human Genes?,”1996, J. Mol. Biol., vol. 262, pp. 459-472.
Samuel Karlin and Chris Burge, “Dinucleotide relative abundance extremes: a genomic signature,”Jul. 1995, TIG, vol. 11, No. 7, pp. 283-290.
Jeffrey G. Lawrence and Howard Ochman, “Molecular archaeology of theEscherichia coligenome,” Aug. 1998, Proc. Natl. Acad. Sci. USA,vol. 95, pp. 9413-9417.
Jeffrey G. Lawrence and Howard Ochman, “Amelioration of Bacterial Genomes: Rates of Change and Exchange,” 1997, J. Mol. Evol., vol. 44, pp. 383-397.
Sean D. Hooper and Otto G. Berg, “Detection of Genes with Atypical Nucleotide Sequence in Microbial Genomes,” 2002, J. Mol. Evol., vol. 54, pp. 365-375.
William S. Hayes and Mark Borodovsky, “How to Interpret an Anonymous Bacterial Genome: Machine Learning Approach to Gene Identification,” 1998, Genome Research, vol. 8, pp. 1154-1171.
Siv G. E. Andersson and C. G. Kurland, “Codon Preferences in Free-Living Microorganisms,” Jun. 1990, Microbiological Reviews, vol. 54, No. 2, pp. 198-210.
Allan Campbell, Jan Mrazek, and Samuel Karlin, “Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA,” Aug. 1999, Proc. Natl. Acad. Sci. USA, vol. 96, pp. 9184-9189.
Santiago Garcia-Vallve, Anton Romeu, and Jaume Palau, “Horizontal Gene Transfer in Bacterial and Archaeal Complete Genomes,” 2000, Genome Research, vol. 10, pp. 1719-1725.
S. Garcia-Vallve, E. Guzman, M. A. Montero, and A. Romeu, “HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes,” 2003, Nucleic Acids Research, vol. 31, No. 1, pp. 187-189.
Paul M. Sharp and Wen-Hsiung Li, “The codon adaptation index—a measure of directional synonymous codon usage bias, and its potential applications,” 1987, Nucleic Acids Research, vol. 15, No. 3, pp. 1281-1295.
Samuel Karlin, Jan Mrazek, and Allan M. Campbell, “Compositional Biases of Bacterial Genomes and Evolutionary Implications,” Jun. 1997, Journal of Bacteriology, vol. 179, No. 12, pp. 3899-3913.
Rigoutsos Isidore
Tsirigos Aristotelis
International Business Machines - Corporation
McGinn IP Law Group PLLC
Smith Carolyn L.
LandOfFree
Apparatus, machine-readable medium, and system for the... does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Apparatus, machine-readable medium, and system for the..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Apparatus, machine-readable medium, and system for the... will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-4061724