Accurate discrimination of conserved coding and non-coding regions through multiple indicators of evolutionary dynamics

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages 282-

  Rè, Matteo ^a   Pesole, Graziano ^b,c   Horner, David S ^a  

^a UNIVERSITY OF MILAN   (Italy)

^b CNR   (Italy)

^c UNIVERSITY OF BARI   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

LEARNING ALGORITHMS; PROTEINS; SUPPORT VECTOR MACHINES;

CONSERVED PROTEINS; EVOLUTIONARY DYNAMICS; GENOME SEQUENCES; MULTIPLE INDICATORS; NON-CODING REGION; NON-CODING SEQUENCES; SEQUENCE HOMOLOGY; SEQUENCE SIMILARITY;

CODES (SYMBOLS);

COMPLEMENTARY DNA;

ACCURACY; ARTICLE; CLASSIFIER; COMPUTER PREDICTION; CONTROLLED STUDY; DNA SEQUENCE; FALSE POSITIVE RESULT; GENOMICS; INFORMATION PROCESSING; MACHINE LEARNING; NUCLEOTIDE SEQUENCE; PROBABILITY; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SUPPORT VECTOR MACHINE;

EID: 70449452925     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-282     Document Type: Article

References (25)

1. Sandelin A. Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. BMC Genomics 2004, 5:99. 10.1186/1471-2164-5-99, 544600, 15613238.
2. Pheasant M, Mattick JS. Raising the estimate of functional human sequences. Genome Res 2007, 17:1245-53. 10.1101/gr.6406307, 17690206.
3. Linial M. How incorrect annotations evolve - the case of short ORFs. Trends Biotech 2003, 21:298-300.
4. Chen CC. Patterns of internal gene duplication in the course of metazoan evolution. Gene 2007, 396:59-65. 10.1016/j.gene.2007.02.021, 17442504.
5. Chen FC. Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to- genome comparisons in human, mouse and rat. BMC Bioinformatics 2006, 7:136. 10.1186/1471-2105-7-136, 1479377, 16536879.
6. Kim H. Expansion of symmetric exon-bordering domains does not explain evolution of lineage specific genes in mammals. Genetica 2006, 131:59-68. 10.1007/s10709-006-9113-6, 17082903.
7. Mignone F. Computational identification of protein coding potential of conserved sequence tags through cross-species evolutionary analysis. Nucleic Acids Res 2003, 31:4639-4645. 10.1093/nar/gkg483, 169873, 12888525.
8. Castrignanò T. CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison. Nucleic Acids Res 2004, (32 web server):W624-627. 10.1093/nar/gkh486, 441624, 15215464.
9. Castrignanò T. GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags. Bioinformatics 2006, 22:497-499. 10.1093/bioinformatics/bti754, 16267081.
10. Nekrutenko A. The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study. Genome Res 2002, 12:198-202. 10.1101/gr.200901, 155263, 11779845.
11. Rogozin IB. Protein-coding regions prediction combining similarity searches and conservative evolutionary properties of protein-coding sequences. Gene 1999, 226:129-137. 10.1016/S0378-1119(98)00509-5, 9889348.
12. Badger JH, Olsen GJ. CRITICA: coding region identification tool invoking comparative analysis. Mol Biol Evol 1999, 16:512-524.
13. Frith MC. Discrimination of Non-Protein-Coding Transcripts from Protein-Coding mRNA. RNA Biol 2006, 3:40-48.
14. The ENCODE project Consortium The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 2004, 306:636-40. 10.1126/science.1105136, 15499007.
15. Hubbard T. The Ensembl genome database project. Nucleic Acids Research 2002, 30:38-41. 10.1093/nar/30.1.38, 99161, 11752248.
16. Chang CC, Lin CJ. LIBSVM: a library for support vector machines. Software 2001, , http://www.csie.ntu.edu.tw/~cjlin/libsvm
17. Delong E. Comparing the areas under two or more correlated Receiver Operating Characteristics Curves: a nonparametric approach. Biometrics 1988, 44:837-845. 10.2307/2531595, 3203132.
18. Vergara IA. StAR: a simple tool for the statistical comparison of ROC curves. BMC Bioinformatics 2008, 9:265. 10.1186/1471-2105-9-265, 2435548, 18534022.
19. Liu J. Distinguishing protein-coding from non-coding RNAs through support vector machines. PLoS Genet 2006, 2:e29. 10.1371/journal.pgen.0020029, 1449884, 16683024.
20. Kong L. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res 2007, 35:W345-349. 10.1093/nar/gkm391, 1933232, 17631615.
21. Matassi G. Chromosomal location effects on gene sequence evolution in mammals. Curr Biol 1999, 9:786-791. 10.1016/S0960-9822(99)80361-3, 10469563.
22. Anastassiou D. Frequency-domain analysis of biomolecular sequences. Bioinformatics 2000, 16:1073-1081. 10.1093/bioinformatics/16.12.1073, 11159326.
23. Tiwari S. Prediction of probable genes by Fourier analysis of genomic sequences. Comput Appl Biosci 1997, 13:263-270.
24. Datta S, Asif A. A fast DFT based gene prediction algorithm for identification of protein coding regions. Proceedings ICASSP 05 2005, 5:v653-656.
25. Schneider A. Empirical codon substitution matrix. BMC Bioinformatics 2005, 6:134. 10.1186/1471-2105-6-134, 1173088, 15927081.