IORI-PseKNC: A predictor for identifying origin of replication with pseudo k-tuple nucleotide composition

Chemometrics and Intelligent Laboratory Systems

Volumn 141, Issue , 2015, Pages 100-106

  Li, Wen Chao ^a   Deng, En Ze ^a   Ding, Hui ^a   Chen, Wei ^b   Lin, Hao ^a  

^a UNIVERSITY OF ELECTRONIC SCIENCE AND TECHNOLOGY OF CHINA   (China)

^b HEBEI UNITED UNIVERSITY   (China)

Author keywords

DNA local structural property; Origin of replication; Pseudo k tuple nucleotide composition; Saccharomyces cerevisiae

Indexed keywords

DINUCLEOTIDE; DNA;

ACCURACY; ARTICLE; COMPUTER PROGRAM; DNA REPLICATION; DNA SEQUENCE; FUNGAL GENOME; GENE AND NUCLEIC ACID PARAMETERS; GENE SEQUENCE; INTERNET; IORI PSEKNC; JACKKNIFE TEST; MATHEMATICAL COMPUTING; NONHUMAN; PREDICTION; PSEUDO K TUPLE NUCLEOTIDE COMPOSITION; QUALITY CONTROL; REPLICATION ORIGIN REGION; SACCHAROMYCES CEREVISIAE; SUPPORT VECTOR MACHINE;

EID: 84920993500     PISSN: 01697439     EISSN: 18733239     Source Type: Journal    
DOI: 10.1016/j.chemolab.2014.12.011     Document Type: Article

References (53)

1. Halazonetis T.D. Conservative DNA replication. Nat. Rev. Mol. Cell Biol. 2014, 15:300.
2. Marczynski G.T., Shapiro L. Bacterial chromosome origins of replication. Curr. Opin. Genet. Dev. 1993, 3:775-782.
3. Schub O., Rohaly G., Smith R.W.P., Schneider A., Dehde S., Dornreiter I.L., Nasheuer H.P. Multiple phosphorylation sites of DNA polymerase alpha-primase cooperate to regulate the initiation of DNA replication in vitro. J. Biol. Chem. 2001, 276:38076-38083.
4. Foureau E., Courdavault V., Gallon S.M.N., Besseau S., Simkin A.J., Creche J., Atehortua L., Giglioli-Guivarc'h N., Clastre M., Papon N. Characterization of an autonomously replicating sequence in Candida guilliermondii. Microbiol. Res. 2013, 168:580-588.
5. Dhar M.K., Sehgal S., Kaul S. Structure, replication efficiency and fragility of yeast ARS elements. Res. Microbiol. 2012, 163:243-253.
6. Crampton A., Chang F., Pappas D.L., Frisch R.L., Weinreich M. An ARS element inhibits DNA replication through a SIR2-dependent mechanism. Mol. Cell 2008, 30:156-166.
7. Tiengwe C., Marques C.A., McCulloch R. Nuclear DNA replication initiation in kinetoplastid parasites: new insights into an ancient process. Trends Parasitol. 2014, 30:27-36.
8. Coin F., Reina-San-Martin B., Giglia-Mari G., Berneburg M. DNA in 3R: repair, replication, and recombination. Mol. Biol. Int. 2012, 2012:658579.
9. Cayrou C., Coulombe P., Puy A., Rialle S., Kaplan N., Segal E., Mechali M. New insights into replication origin characteristics in metazoans. Cell Cycle 2012, 11:658-667.
10. Valovka T., Schonfeld M., Raffeiner P., Breuker K., Dunzendorfer-Matt T., Hartl M., Bister K. Transcriptional control of DNA replication licensing by Myc. Sci. Rep. 2013, 3:9.
11. Martin M.M., Ryan M., Kim R., Zakas A.L., Fu H., Lin C.M., Reinhold W.C., Davis S.R., Bilke S., Liu H., Doroshow J.H., Reimers M.A., Valenzuela M.S., Pommier Y., Meltzer P.S., Aladjem M.I. Genome-wide depletion of replication initiation events in highly transcribed regions. Genome Res. 2011, 21:1822-1832.
12. Lubelsky Y., MacAlpine H.K., MacAlpine D.M. Genome-wide localization of replication factors. Methods 2012, 57:187-195.
13. Van Houten J.V., Newlon C.S. Mutational analysis of the consensus sequence of a replication origin from yeast chromosome III. Mol. Cell. Biol. 1990, 10:3917-3925.
14. Marsolier-Kergoat M.C. Asymmetry indices for analysis and prediction of replication origins in eukaryotic genomes. PLoS ONE 2012, 7:e45050.
15. Yin S., Deng W., Hu L., Kong X. The impact of nucleosome positioning on the organization of replication origins in eukaryotes. Biochem. Biophys. Res. Commun. 2009, 385:363-368.
16. Eaton M.L., Galani K., Kang S., Bell S.P., MacAlpine D.M. Conserved nucleosome positioning defines replication origins. Genes Dev. 2010, 24:748-753.
17. Mechali M. Eukaryotic DNA replication origins: many choices for appropriate answers. Nat. Rev. Mol. Cell Biol. 2010, 11:728-738.
18. Nieduszynski C.A., Knox Y., Donaldson A.D. Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev. 2006, 20:1874-1879.
19. Brukner I., Sanchez R., Suck D., Pongor S. Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides. EMBO J. 1995, 14:1812-1818.
20. Bishop E.P., Rohs R., Parker S.C., West S.M., Liu P., Mann R.S., Honig B., Tullius T.D. A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA. ACS Chem. Biol. 2011, 6:1314-1320.
21. Kang J.H., Kim S.M. DNA cleavage by hydroxyl radicals generated in the Cu, Zn-superoxide dismutase and hydrogen peroxide system. Mol. Cell 1997, 7:777-782.
22. Chen W., Feng P., Lin H. Prediction of replication origins by calculating DNA structural properties. FEBS Lett. 2012, 586:934-938.
23. 2O)(2) (2+) of 2,2'-biimidazole. Bull. Korean Chem. Soc. 2013, 34:3695-3702.
24. Guo S.-H., Deng E.-Z., Xu L.-Q., Ding H., Lin H., Chen W., Chou K.-C. iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition. Bioinformatics (Oxford, England) 2014, 30:1522-1529.
25. Chen W., Feng P.M., Lin H., Chou K.C. iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition. Nucleic Acids Res. 2013, 41:e68.
26. Zuo Y., Zhang P., Liu L., Li T., Peng Y., Li G., Li Q. Sequence-specific flexibility organization of splicing flanking sequence and prediction of splice sites in the human genome. Chromosome Research: An International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology 2014.
27. Jimenez-Useche I., Yuan C. The effect of DNA CpG methylation on the dynamic conformation of a nucleosome. Biophys. J. 2012, 103:2502-2512.
28. Hizume K., Yagura M., Araki H. Concerted interaction between origin recognition complex (ORC), nucleosomes and replication origin DNA ensures stable ORC-origin binding. Genes Cells 2013, 18:764-779.
29. Nieduszynski C.A., Hiraga S., Ak P., Benham C.J., Donaldson A.D. OriDB: a DNA replication origin database. Nucleic Acids Res. 2007, 35:D40-D46.
30. Li W., Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22:1658-1659.
31. Lin H., Li Q.Z. Eukaryotic and prokaryotic promoter prediction using hybrid approach. Theory Biosci. 2011, 130:91-100.
32. Zhou X., Li Z., Dai Z., Zou X. Predicting methylation status of human DNA sequences by pseudo-trinucleotide composition. Talanta 2011, 85:1143-1147.
33. Guo F.B., Ou H.Y., Zhang C.T. ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes. Nucleic Acids Res. 2003, 31:1780-1789.
34. Li Q.Z., Lin H. The recognition and prediction of sigma70 promoters in Escherichia coli K-12. J. Theor. Biol. 2006, 242:135-141.
35. Chen W., Feng P.-M., Lin H., Chou K.-C. iSS-PseDNC: identifying splicing sites using pseudo dinucleotide composition. BioMed. Res. Int. 2014, 2014:12.
36. Chen W., Lei T.Y., Jin D.C., Lin H., Chou K.C. PseKNC: a flexible web server for generating pseudo k-tuple nucleotide composition. Anal. Biochem. 2014, 456:53-60.
37. Zuo Y.C., Li Q.Z. The hidden physical codes for modulating the prokaryotic transcription initiation. Phys. A 2010, 389:4217-4223.
38. Soltani S., Askari H., Ejlali N., Aghdam R. The structural properties of DNA regulate gene expression. Mol. BioSyst. 2014, 10:273-280.
39. Jensen L.J., Bateman A. The rise and fall of supervised machine learning techniques. Bioinformatics 2011, 27:3331-3332.
40. Zhang Y.X. An improved QSPR method based on support vector machine applying rational sample data selection and genetic algorithm-controlled training parameters optimization. Chemometr. Intell. Lab. Syst. 2014, 134:34-46.
41. Huang X., Cao D.S., Xu Q.S., Shen L., Huang J.H., Liang Y.Z. A novel tree kernel support vector machine classifier for modeling the relationship between bioactivity and molecular descriptors. Chemometr. Intell. Lab. Syst. 2013, 120:71-76.
42. Nantasenamat C., Srungboonmee K., Jamsak S., Tansila N., Isarankura-Na-Ayudhya C., Prachayasittikul V. Quantitative structure-property relationship study of spectral properties of green fluorescent protein with support vector machine. Chemometr. Intell. Lab. Syst. 2013, 120:42-52.
43. Vapnik V.N. The Nature of Statistical Learning Theory 1995, Springer, New York.
44. Lin H., Chen W., Ding H. AcalPred: a sequence-based tool for discriminating between acidic and alkaline enzymes. PLoS ONE 2013, 8:6.
45. Feng P.M., Chen W., Lin H., Chou K.C. iHSP-PseRAAAC: identifying the heat shock protein families using pseudo reduced amino acid alphabet composition. Anal. Biochem. 2013, 442:118-125.
46. Feng P.M., Lin H., Chen W. Identification of antioxidants from sequence information using Naive Bayes. Comput. Math. Meth. Med. 2013, 2013. ID 567529.
47. Zhang X.Y., Asiedu C.K., Supakar P.C., Khan R., Ehrlich K.C., Ehrlich M. Binding sites in mammalian genes and viral gene regulatory regions recognized by methylated DNA-binding protein. Nucleic Acids Res. 1990, 18:6253-6260.
48. Costa R.H., Grayson D.R., Xanthopoulos K.G., Darnell J.E. A liver-specific DNA-binding protein recognizes multiple nucleotide sites in regulatory regions of transthyretin, alpha 1-antitrypsin, albumin, and simian virus 40 genes. Proc. Natl. Acad. Sci. U. S. A. 1988, 85:3840-3844.
49. Cogoi S., Paramasivam M., Spolaore B., Xodo L.E. Structural polymorphism within a regulatory element of the human KRAS promoter: formation of G4-DNA recognized by nuclear proteins. Nucleic Acids Res. 2008, 36:3765-3780.
50. Ozoline O.N., Deev A.A., Trifonov E.N. DNA bendability-a novel feature in E. coli promoter recognition. J. Biomol. Struct. Dyn. 1999, 16:825-831.
51. Trifonov E.N. Base pair stacking in nucleosome DNA and bendability sequence pattern. J. Theor. Biol. 2010, 263:337-339.
52. Gabdank I., Barash D., Trifonov E.N. Nucleosome DNA bendability matrix (C. elegans). J. Biomol. Struct. Dyn. 2009, 26:403-411.
53. Muller C.A., Hawkins M., Retkute R., Malla S., Wilson R., Blythe M.J., Nakato R., Komata M., Shirahige K., de Moura A.P.S., Nieduszynski C.A. The dynamics of genome replication using deep sequencing. Nucleic Acids Res. 2014, 42:11.