An exon/intron disparity framework based on the nucleotide profile of single sequence

Network Modeling and Analysis in Health Informatics and Bioinformatics

Volumn 1, Issue 1-2, 2012, Pages 19-25

  Liou, Sing Wu ^a   Huang, Yin Fu ^a  

^a NATIONAL YUNLIN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE;

ALTERNATIVE RNA SPLICING; ARABIDOPSIS; ARTICLE; CAENORHABDITIS ELEGANS; CONCEPTUAL FRAMEWORK; DROSOPHILA; EXON; FREQUENCY ANALYSIS; GENETIC CODE; GENETIC HETEROGENEITY; HUMAN; INTRON; LIGATION; META ANALYSIS; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN SYNTHESIS; RNA SEQUENCE;

EID: 85049140044     PISSN: None     EISSN: 21926670     Source Type: Journal    
DOI: 10.1007/s13721-012-0007-5     Document Type: Article

References (32)

1. Arquèsa DG, Michel CJ (1996) A complementary circular code in the protein coding genes. J Theor Biol 182(1): 45-58.
2. Asuncion A, Newman D (2007) UCI machine learning repository.
3. Barash Y, Calarco JA, Gao W, Pan Q, Wang X, Shai O, Blencowe BJ, Frey BJ (2010) Deciphering the splicing code. Nature 465(7294): 53-59.
4. Bortfeldt R, Schindler S, Szafranski K, Schuster S, Holste D (2008) Comparative analysis of sequence features involved in the recognition of tandem splice sites. BMC Genomics 9: 202.
5. Bulmer M (1987) A statistical analysis of nucleotide sequences of introns and exons in human genes. Mol Biol Evol 4(4): 395-405.
6. Burset M, Seledtsov IA, Solovyev VV (2001) SpliceDB: database of canonical and non-canonical mammalian splice sites. Nucleic Acids Res 29(1): 255-259.
7. Chen L, Xuan J, Wang C, Wang Y, Shih I-M, Wang T-L, Zhang Z, Clarke R, Hoffman EP (2009) Biomarker identification by knowledge-driven multilevel ica and motif analysis. Int J Data Min Bioinform 3(4): 365-381.
8. Claverie J-M, Bougueleret L (1986) Heuristic informational analysis of sequences. Nucleic Acids Res 14(1): 179-196.
9. Claverie J-M, Sauvaget I, Bougueleret L (1990) K-tuple frequency analysis: from intron/exon discrimination to t-cell epitope mapping. Methods Enzymol 183: 237-252.
10. Eskesen ST, Eskesen FN, Ruvinsky A (2004) Natural selection affects frequencies of ag and gt dinucleotides at the 5′ and 3′ ends of exons. Genetics 167(1): 543-550.
11. Gopalan V, Tan TW, Lee BTK, Ranganathan S (2004) Xpro: database of eukaryotic protein-encoding genes. Nucleic Acids Res 32(Database issue): D59-63.
12. Liou S-W, Huang Y-F (2008) Investigating the intrinsic differences in flank regions of exon-intron junction sites. International Conference on biomedical engineering and informatics (BMEI'08), vol 2, pp 96-101.
13. Liou S-W, Huang Y-F (2009) Identifying new sequence features for exon-intron discrimination by rescaled-range frameshift analysis. International Conference on computational and systems biology (ICCSB'09), vol 37, pp 349-353.
14. Louie E, Ott J, Majewski J (2003) Nucleotide frequency variation across human genes. Genome Res 13(12): 2594-2601.
15. Luo L, Ji F (1997) The preferential mode analysis of DNA sequence. J Theor Biol 188(3): 343-353.
16. Malousi A, Chouvarda I, Koutkias V, Kouidou S, Maglaveras N (2010) SpliceIT: a hybrid method for splice signal identification based on probabilistic and biological inference. J Biomed Inform 43(2): 208-217.
17. Mengeritsky G, Smith TF (1989) New analytical tool for analysis of splice site sequence determinants. Comput Appl Biosci 5(2): 97-100.
18. Nakata K, Kanehisa M, DeLisi C (1985) Prediction of splice junctions in mRNA sequences. Nucleic Acids Res 13(14): 5327-5340.
19. Nikolaou C, Almirantis Y (2003) Mutually symmetric and complementary triplets: differences in their use distinguish systematically between coding and non-coding genomic sequences. J Theor Biol 223(4): 477-487.
20. Nikolaou C, Almirantis Y (2004) Measuring the coding potential of genomic sequences through a combination of triplet occurrence patterns and RNY preference. J Mol Evol 59(3): 309-316.
21. Orlov YL, Potapov VN (2004) Complexity: an internet resource for analysis of DNA sequence complexity. Nucleic Acids Res 32(Web Server issue): W628-W633.
22. Parmley JL, Hurst LD (2007) Exonic splicing regulatory elements skew synonymous codon usage near intron-exon boundaries in mammals. Mol Biol Evol 24(8): 1600-1603.
23. Pollastro P, Rampone S (2002) HS3D: Homo sapiens splice site data set. Nucleic Acids Res (Annual Database Issue).
24. Solovyev VV, Salamov AA, Lawrence CB (1994) Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames. Nucleic Acids Res 22(24): 5156-5163.
25. Staden R, McLachlan AD (1982) Codon preference and its use in identifying protein coding regions in long DNA sequences. Nucl Acids Res 10(1): 141-156.
26. Wang Z, Burge CB (2008) Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA 14(5): 802-813.
27. Weir M, Rice M (2004) Ordered partitioning reveals extended splice-site consensus information. Genome Res 14(1): 67-78.
28. Willie E, Majewski J (2004) Evidence for codon bias selection at the pre-mRNA level in eukaryotes. Trends Genet 20(11): 534-538.
29. Zhang C-T (1997) A symmetrical theory of DNA sequences and its applications. J Theor Biol 187(3): 297-306.
30. Zhang MQ (1998) Statistical features of human exons and their flanking regions. Hum Mol Genet 7(5): 919-932.
31. Zhang XH-F, Leslie CS, Chasin LA (2005) Dichotomous splicing signals in exon flanks. Genome Res 15(6): 768-779.
32. Zhuo D, Madden R, Elela SA, Chabot B (2007) Modern origin of numerous alternatively spliced human introns from tandem arrays. Proc Natl Acad Sci USA 104(3): 882-886.