Identification and Measurement of Neighbor Dependent Nucleotide Substitution Processes

Lecture Notes in Informatics (LNI), Proceedings - Series of the Gesellschaft fur Informatik (GI)

Volumn P-53, Issue , 2004, Pages 227-234

  Arndt, Peter F ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DINUCLEOTIDES; FRUITFLIES; MEASUREMENTS OF; NUCLEOTIDE SUBSTITUTION; REALISTIC MODEL; ZEBRAFISH;

EID: 21244442555     PISSN: 16175468     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (14)

1. [ABH02] Arndt, P. F., Burge, C. B. and Hwa, T. (2002). DNA Sequence Evolution with Neighbor-Dependent Mutation. 6th Annual International Conference on Computational Biology RECOMB2002, Washington DC, ACM Press, KK.
2. [APH03] Arndt, P. F., Petrov, D. A. and Hwa, T. (2003). Distinct changes of genomic biases in nucleotide substitution at the time of Mammalian radiation. Mol Biol Evol 20(11): 1887-96.
3. [Bo66] Box, M. J. (1966). A Comparison of Several Current Optimization Methods and Use of Transformations in Constrained Problems. Computer Journal 9(1): 67-77.
4. [Co78] Coulondre, C., Miller, J. H., Farabaugh, P. J., et al. (1978). Molecular basis of base substitution hotspots in Escherichia coli. Nature 274(5673): 775-80.
5. [DZC97] Douki, T., Zalizniak, T. and Cadet, J. (1997). Far-UV-induced dimeric photoproducts in short oligonucleotides: sequence effects. Photochem Photobiol 66(2): 171-9.
6. [EG01] Ewens, W. J. and Grant, G. (2001). Statistical methods in bioinformatics: an introduction. New York, Springer.
7. [CB95] Karlin, S. and Burge, C. (1995). Dinucleotide relative abundance extremes: a genomic signature. Trends Genet 11(7): 283-90.
8. [KM97] Karlin, S. and Mrazek, J. (1997). Compositional differences within and between eukaryotic genomes. Proc Natl Acad Sci U S A 94(19): 10227-32.
9. [KMC97] Karlin, S., Mrazek, J. and Campbell, A. M. (1997). Compositional biases of bacterial genomes and evolutionary implications. J Bacteriol 179(12): 3899-913.
10. [LH04] Lunter, G. and Hein, J. (2004). A nucleotide substitution model with nearest-neighbour interactions. Bioinformatics.
11. [Pr92] Press, W. H., Teukolsky, S. A., Vetterling, W. T., et al. (1992). Numerical Recipes in C, The art of scientific computing. Cambridge, Cambridge University Press.
12. [RR80] Razin, A. and Riggs, A. D. (1980). DNA methylation and gene function. Science 210(4470): 604-10.
13. [Ru76] Russell, G. J., Walker, P. M., Elton, R. A., et al. (1976). Doublet frequency analysis of fractionated vertebrate nuclear DNA. J Mol Biol 108(1): 1-23.
14. [RS77] Russell, G. J. and Subak-Sharpe, J. H. (1977). Similarity of the general designs of protochordates and invertebrates. Nature 266(5602): 533-6.