Reassembly of DNA Fragments using Row Access Method
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Jared T. Simpson and Richard Durbin, “Efficient construction of an assembly string graph using the FM-index”, Vol. 26 ISMB 2010, pages i367–i373.
Michael James Clark1, Nils Homer, Brian D. O‟Connor, Zugen Chen, Ascia Eskin, Hane Lee, “U87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line”, PLoS Genetics, January 2010 , Volume 6 , Issue 1 , e1000832.
Nils Homer, Barry Merriman and Stanley F Nelson, Local alignment of two-base encoded DNA sequence, BMC Bioinformatics 2009, 10:175 doi:10.1186/1471-2105-10-175.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan3, Nils Homer, 2009, BIOINFORMATICS APPLICATIONS NOTE Vol. 25 no. 16 2009, pages 2078–2079.
Lori Giver and Frances H Arnold, Combinatorial protein design by in vitro recombination,Combinatorial chemistry, 1998, PP 335-339.
Allawi, H. & SantaLucia Jr, J., “ Thermodynamics and NMR of internal G T mismatches in DNA. Biochemistry”, 1996,36, 10581–10594.
Allawi, H. & SantaLucia Jr, J. , “Nearest neighbor thermodynamic parameters for internal G A mismatches in DNA”,1997, Biochemistry 37, 2170–2179.
Allawi, H. & SantaLucia Jr, J. , “ Nearestneighbor thermodynamics of internal A C mismatches in DNA: sequence dependence and pH effects”, 1997, Biochemistry 37, 9435–9444.
Allawi, H. & SantaLucia Jr, J., “. Thermodynamics of internal C T mismatches in DNA”,1998, Nucleic Acids Res. 26, 2694–2701.
Crameri, A., Raillard, S., Bermudez, E. & Stemmer, W., “ DNA shuffling of a family of genes from diverse species accelerates directed evolution”, 1998, Nature 391, 288–291.
Moore, G. & Maranas, C. “ Modeling DNA mutation and recombination for directed evolution experiments”,2000, J. theor. Biol. 205, 483–503, doi:10.1006/ jtbi.2000.2082.
Moore, G., Maranas, C., Lutz, S. & Benkovic, S. ,“ Predicting crossover generation in DNA shuffling.”, 2001, Proc. Natl Acad. Sci. U.S.A. 98, 3226–3231.
Nakano, S., Fujimoto, M. & Sugimoto, H. H. N.,” Nucleic acid duplex stability: influence of base composition on cation effect”, 2000, Nucleic Acids Res. 27, 2957–2965.
Ness, J., Welch, M., Giver, L., Bueno, M., Cherry, J., Borchert, T., Stemmer, W. & Minshull, L., “DNA shuffling of subgenomic sequences of subtilisin”,1999, Nature Biotech. 17, 893–896.
SantaLucia Jr, J. , ”A unified view of polymer, dumbbell, and oligonucleotide DNA nearest neighbor thermodynamics”, 1999, . Proc. Natl Acad. Sci. U.S.A. 95, 1460–1465.
Stemmer, W., “DNA shuffling by randomfragm entation and reassembly: in vitro recombination for molecular evolution”, 1999, Proc. Natl Acad. Sci. U.S.A. 91, 10747–10751.
Liu Xikui, Li Yan, “Some Notes on 2-D Graphical Representation of DNA Sequence” Proceedings of the 27th Chinese Control ConferenceJuly 16–18, 2008, Kunming, Yunnan, China.
HAMORI J, RUSKIN J. H curves - A novel method of representation of nucleotide series especially suited for long DNA sequences[J]. J. Bio.Chem, 1983, 258: 1318-1327.
GATES M A. A simple way to look at DNA[J]. J. Theor. Biol. 1986, 119: 319-328.
NANDY A. A new graphical representation and analysis of DNA sequence structure I. Methodology and application to globin genes[J]. Curr. Sci. 1994, 66: 309-313.
NANDY A. Graphical analysis of DNA sequence structure:III. Indications of evolutionary distinctions and characteristics of intros and exons[J]. Curr. Sci. 1996, 70: 611-668.
LEONG P M, MORGENTHALER S. Random walk and gap plots of DNA sequences[J]. Comput. Applic. Biosci. 1995, 11: 503-507.
NANDY A, NANDY P. Graphical analysis of DNA sequence structure II: Relative abundances of nucleotides in DNAs, gene evolution and duplication[J]. Curr. Sci. 1995, 68:75-8
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