A genome signature based on Markov modeling

Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings

Volumn 7 VOLS, Issue , 2005, Pages 2832-2835

  Li, Jian ^a   Sayood, Khalid ^a  

^a UNIVERSITY OF NEBRASKA LINCOLN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DATA PROCESSING; GENES; MARKOV PROCESSES; MATHEMATICAL MODELS; PROBLEM SOLVING;

DATA PREPROCESSING; GENOME DATA; GENOME SIGNATURES; MARKOV MODELING;

GENETIC ENGINEERING;

EID: 33846926591     PISSN: 05891019     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (14)

1. Samuel Karlin and Chris Burge, "Dinucleotide relative abundance extremes: a genomic signature," Trends in Genetics, Vol. 11, Issue 7, July 1995, PP 283-290.
2. Samuel Karlin, "Bacterial DNA strand compositional asymmetry," Trends in Microbiology, Vol. 7, Issue 8, 1 August 1999, PP 305-308.
3. Campbell, Allan and Mrazek, Jan and Karlin, Samuel, "Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA,"PNAS,Vol. 96, Issue 16, August 1999,PP 9184-9189.
4. Srabashi Basu, Debi Prosad Burma, Probal Chaudhuri, "Words in DNA sequences: some case studies based on their frequency statistics," Journal of Mathematical Biology, Vol. 46, Issue 6, Jun 2003, PP 479-503.
5. Hao B, Qi J., "Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance," J. Bioinform. Comput. Biol., 2004 Mar;2(1):1-19.
6. Deschavanne, P.J., Giron, A., Vilain, J., Fagot, G., Fertil, B., "Genomic signuture: characterization and classification of species assessed by chaos game representation of sequences," Molecular Biology and Evolution,1999: 16, PP 1391C 1399.
7. Roderic DM Page, Edward C. Holmes. Molecular Evolution: A Phylogenetic Approach, Blackwell Science, Inc. 1998, ch. 2.
8. Jian Li, Markov models and bacterial genomes [thesis], Univeristy of Nebraska-Lincoln, 2005. Available:Univeristy of Nebraska-Lincoln.
9. A. Carbone, F. Kepes, and A. Zinovyev.,"Codon bias signatures, organization of microorganisms in codon space, and lifestyle," Mol. Biol. Evol., March, 2005; 22(3): 547-561.
10. Samuel Karlin and Lon R. Cardon, "Computational DNA Sequence Analysis," Annu. Rev. Microbiol., 1994. 48:619-54.
11. Chen, Swaine L. and Lee, William and Hottes, Alison K. and Shapiro, Lucy and McAdams, Harley H., "Codon usage between genomes is constrained by genome-wide mutational processes", PNAS,vol.101, Issue 10, 2004, PP 3480-3485.
12. Diane L. Rowe, and Rodney L. Honeycutt, "Phylogenetic Relationships, Ecological Correlates, and Molecular Evolution Within the Cavioidea (Mammalia, Rodentia)", Mol. Biol. Evol. 19: 263-277.
13. Otu HH, Sayood K., "A new sequence distance measure for phylogenetic tree construction", BIOINFORMATICS 19 (16): 2122-2130 NOV 1 2003.
14. Trillmich F, Kraus C, Kunkele J, et al., "Species-level differentiation of two cryptic species pairs of wild cavies, genera Cavia and Galea, with a discussion of the relationship between social systems and phylogeny in the Caviinae", CAN J ZOOL 82 (3): 516-524 MAR 2004.