Statistical measures of the structure of genomic sequences: Entropy, complexity, and position information

Journal of Bioinformatics and Computational Biology

Volumn 4, Issue 2, 2006, Pages 523-536

  Orlov, Yuriy L ^a,d   Te Boekhorst, Rene ^b   Abnizova, Irina I ^c  

^a INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

^b UNIVERSITY OF HERTFORDSHIRE   (United Kingdom)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d GENOME INSTITUTE OF SINGAPORE   (Singapore)

Author keywords

Complexity; Entropy; Exons; Introns; Regulatory regions; Sequence analysis

Indexed keywords

PALINDROMIC DNA; TRANSCRIPTION FACTOR;

BINDING SITE; BIOINFORMATICS; COMPUTER PROGRAM; CONFERENCE PAPER; DNA SEQUENCE; ENTROPY; GENE IDENTIFICATION; GENE SEQUENCE; GENE STRUCTURE; GENETIC CODE; GENOME ANALYSIS; INTRON; LINGUISTICS; MATHEMATICAL COMPUTING; PROMOTER REGION; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; TANDEM REPEAT;

ALGORITHMS; BASE SEQUENCE; CHROMOSOME MAPPING; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; ENTROPY; MODELS, GENETIC; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 33745726566     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720006001801     Document Type: Conference Paper

References (28)

1. Abe T, Kanaya S, Kinouchi M, et al., Informatics for unveiling hidden genome signatures, Genome Res 13(4):693-702, 2003.
2. Wan H, Li L, Federhen S, Wootton JC, Discovering simple regions in biological sequences associated with scoring schemes, J Comput Biol 10(2):171-185, 2003.
3. Li W, The complexity of DNA, Complexity 3:33-37, 1997.
4. Mantegna RN, Buldyrev SV, Buldyrev AL, et al., Linguistic features of noncoding DNA sequences, Phys Rev Lett 73:3169-3172, 1994.
5. Azbel YM, Universality in a DNA statistical structure, Phys Rev Lett 75:68-171, 1995.
6. Krogh A, Mian S, Haussler D, A hidden Markov model that finds genes in E. coli DNA, Nucleic Acids Res 22:4768-4778, 1994.
7. Voss R, Evolution of long-range fractal correlations and 1/f noise in DNA base sequences, Phys Rev Lett 68:3805-3808, 1992.
8. Cao Y, Tung WW, Tung JB, Qi Y, Recurrence time statistics: Versatile tools for genomic DNA sequence analysis, J Bioinform Comput Biol 3(3):677-696, 2005.
9. Peng CK, Buldyrev SV, Havlin S, et al., Mosaic organization of nucleotides, Phys Rev E 1:1685-1689, 1994.
10. Herzel H, Herzel I, Correlations in DNA sequences: The role of protein coding segments, Phys Rev E 55:800-810, 1997.
11. Abnizova I, Schilstra M, te Boekhorst R, Nehaniv CL, A statistical approach to distinguish between different DNA functional parts, WSEAS Trans Comput Methods 2(4):1188-1196, 2003.
12. Hancock JM, Genome size and the accumulation of simple sequence repeats: implications of new data from genome sequencing projects, Genetica 115:93-103, 2002.
13. Wootton JC, Federhen S, Analysis of compositionally biased regions in sequence databases, Methods Enzymol 266:554-571, 1996.
14. Troyanskaya OG, Arbell O, Koren Y, et al., Sequence complexity profiles of prokaryotic genomic sequences: A fast algorithm for calculating linguistic complexity, Bioinformatics 18:679-688, 2002.
15. Gusev VD, Nemytikova LA, Chuzhanova NA, On the complexity measures of genetic sequences, Bioinformatics 15:994-999, 1999.
16. Lempel A, Ziv J, On the complexity of finite sequences, IEEE Trans Inf Theory IT 22:75-81, 1976.
17. Orlov YL, Orlov VD, Miroshnichenko LA, LZcomposer: Decomposition of genomic sequences by repeat fragments, Biofizika (Mosk) 48(Suppl. 1):7-16, 2003.
18. Orlov YL, Potapov VN, Complexity: An internet resource for analysis of DNA sequence complexity, Nucleic Acids Res 32(Web Server issue): W62 8-W633, 2004.
19. Bolshoy A, DNA sequence analysis linguistic tools: Contrast vocabularies, compositional spectra and linguistic complexity, Appl Bioinformatics 2(2):103-112, 2003.
20. Gabrielian A, Bolshoy A, Sequence complexity and DNA curvature, Comput Chem 23(3-4):263-274, 1999.
21. Trifonov EN, Making sense of the human genome, in Sarma RH, Sarma MH (eds.) Structure & Methods, Adenine Press, Albany, Vol. 1, pp. 69-77, 1990.
22. Rosas A, Nogueira E Jr, Fontanari JF, Multilractal analysis of DNA walks and trails, Phys Rev E Stat Nonlin Soft Matter Phys 66(6 Pt 1): 061906, 2002.
23. Schroeder M, Fractals, Chaos, Power Laws. Minutes from an infinite paradise, Freeman, New York, 1991.
24. Kolchanov NA, Ignatieva EV, Ananko EA, et al., Transcription Regulatory Regions Database (TRRD): Its status in 2002, Nucleic Acids Res 30(1):312-317, 2002.
25. Praz V, Perier RC, Bonnard C, Bucher P, The Eukaryotic Promoter Database, EPD: New entry types and links to gene expression data, Nucleic Acids Res 30:322-324, 2002.
26. Burset M, Seledtsov IA, Solovyev VV, SpliceDB: Database of canonical and noncanonical mammalian splice sites, Nucleic Acids Res 29(1):255-259, 2001.
27. Saxonov S, Daizadeh I, Fedorov A, Gilbert W, EID: The Exon-Intron Database-an exhaustive database of protein-coding intron-containing genes, Nucleic Acids Res 28(1):185-190, 2000.
28. Trifonov EN, Genetic level of DNA sequences is determined by superposition of many codes, Mol Biol (Mosk) 31(4):759-767, 1997; in Russian.