Computational identification of protein-coding sequences by comparative analysis

Proceedings - 2007 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2007

Volumn , Issue , 2007, Pages 95-102

  Fontaine, Arnaud ^a   Touzet, Hélène ^a  

^a ECOLE CENTRALE DE LILLE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCOMMUNICATIONS; BIOINFORMATICS; INFORMATION SCIENCE;

CODING SEQUENCES; COMPARATIVE ANALYSIS; COMPARATIVE GENOMICS; COMPUTATIONAL IDENTIFICATION; GENE FINDING; GENE PREDICTION; HOMOLOGY SEARCH; INTERNATIONAL CONFERENCES; PROTEIN-CODING; STATISTICAL PROPERTIES; SUBSTITUTION PATTERNS;

PROGRAMMING THEORY;

EID: 49049101878     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBM.2007.11     Document Type: Conference Paper

References (35)

1. S. Altschul, T. Madden, A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. Lipman. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nuc. Ac. Res., 25(17):3389-3402, 1997.
2. A. Bairoch, B. Boeckmann, S. Ferro, and E. Gasteiger. Swiss-Prot: Juggling between evolution and stability. Briefings in Bioinformatics, 5(1):39-55, 2004.
3. E. Birney, M. Clamp, and R. Durbin. Genewise and genome-wise. Gen. Res., 14(5):988-995, 2004.
4. M. Blanchette, W. Kent, C. Riemer, L. Elnitski, A. Smit, K. Roskin, R. Baertsch, K. Rosenbloom, H. Clawson, E. Green, D. Haussler, and W. Miller. Aligning multiple genomic sequences with the threaded blockset aligner. Gen. Res., 14(4):708-723, April 2004.
5. D. Boffelli, J. McAuliffe, D. Ovcharenko, K. Lewis, I. Ovcharenko, L. Pachter, and E. Rubin. Phylogenetic shadowing of primate sequences to find functional regions of the human genomes. Science, 299(5611):1391-1394, 2003.
6. C. Burge and S. Karlin. Prediction of complete gene structures in human genomic dna. Jour. of Mol. Biol., 268(1):78-94, 1997.
7. T. Castrignan, A. Canali, G. Grillo, S. Liuni, F. Mignone, and G. Pesole. CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison. Nuc. Ac. Res., 32:W624-W627, 2004.
8. D. Cora, C. Herrmann, C. Dieterich, F. Di Cunto, P. Provero, and M. Caselle. Ab initio identification of putative human transcription factor binding sites by comparative genomics. BMC Bioinfo., 6:110, 2005.
9. J. H. Do and D.-K. Choi. Computational approaches to gene prediction. J Microbiol, 44(2):137-144, 2006.
10. R. D. Finn, J. Mistry, B. Schuster-Bockler, S. Griffiths-Jones, V. Hollich, T. Lassmann, S. Moxon, M. Marshall, A. Khanna, R. Durbin, S. R. Eddy, E. L. L. Sonnhammer, and A. Bateman. Pfam: clans, web tools and services. Nuc. Ac. Res., 34:D247-D251, 2006.
11. S. Griffiths-Jones, S. Moxon, M. Marshall, A. Khanna, S. R. Eddy, and A. Bateman. Rfam: annotating non-coding RNAs in complete genomes. Nuc. Ac. Res., 33:D121-D124, 2005.
12. S. S. Gross and M. R. Brent. Using multiple alignments to improve gene prediction. Jour. of Comp. Biol., 13(2):379-393, March 2006.
13. S. Henikoff and J. G. Henikoff. Amino acid substitution matrices from protein blocks. PNAS, 89:10915-10919, November 1992.
14. D. Karolchik, R. Baertsch, M. Diekhans, T. Furey, A. Hinrichs, Y. Lu, K. Roskin, M. Schwartz, C. Sugnet, D. Thomas, R. Weber, D. Haussler, and W. Kent. The UCSC Genome Browser Database. Nuc. Ac. Res., 31(1):51-54, 2003.
15. K. Liolios, N. Tavernarakis, P. Hugenholtz, and N. C. Kyrpides. The genomes on line database (gold) v.2: a monitor of genome projects worldwide. Nuc. Ac. Res., 34:D332-D334, 2006.
16. Y. Liu, X. S. Liu, L. Wei, R. B. Altman, and S. Batzoglou. Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Gen. Res., 14(3):451-458, 2004.
17. A. V. Lukashin and M. Borodovsky. GeneMark.hmm: new solution for gene finding. Nuc. Ac. Res., 26(4):1107-1115, 1998.
18. C. Mathe, M.-F. Sagot, T. Schiex, and P. Rouze. Current methods of gene prediction, their strengths and weaknesses. Nuc. Ac. Res., 30(19):4103-4117, 2002.
19. S. Needleman and C. Wunsch. A general method applicable to the search for similarities in the amino acid sequence of two proteins. Jour. of Mol. Biol., 48(3):443-453, 1970.
20. G. Parra, E. Blanco, and R. Guigò. GeneID in Drosophilia. Gen. Res., 10(4):511-515, April 2000.
21. E. Rivas and S. R. Eddy. Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinfo., 2(1):8, 2001.
22. S. Schwartz, W. J. Kent, A. Smit, Z. Zhang, R. Baertsch, R. C. Hardison, D. Haussler, and W. Miller. Human-mouse alignments with blastz. Gen. Res., 13(1):103-107, 2003.
23. A. Siepel, G. Bejerano, J. Pedersen, A. Hinrichs, M. Hou, K. Rosenbloom, H. Clawson, J. Spieth, L. Hillier, S. Richards, G. Weinstock, R. K. Wilson, R. Gibbs, W. Kent, W. Miller, and D. Haussler. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Gen. Res., 15:1034-1050, 2005.
24. A. Siepel and D. Haussler. Computational identification of evolutionarily conserved exons. In RECOMB '04 proceedings, pages 177-186, New York, NY, USA, 2004. ACM Press.
25. A. Siepel and D. Haussler. Phylogenetic hidden Markov models. In R. Nielsen, editor, Statistical Methods in Molecular Evolution, pages 325-351. Springer, New York, 2005.
26. M. Stanke, O. Keller, I. Gunduz, A. Hayes, S. Waack, and B. Morgenstern. AUGUSTUS: ab initio prediction of alternative transcripts. Nuc. Ac. Res., 34(suppl 2):W435-W439, 2006.
27. M. Stanke, A. Tzvetkova, and B. Morgenstern. AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome. Gen. Biol., 7:S11, August 2006.
28. J. Thompson, D. Higgins, and T. Gibson. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nuc. Ac. Res., 22(22):4673-4680, 1994.
29. J. Uspensky. Introduction to Mathematical Probability. NewYork:McGraw-Hill, 1937.
30. S. Washietl and I. L. Hofacker. Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. Jour. of Mol. Biol., 342:19-30, 2004.
31. S. Washietl, I. L. Hofacker, M. Lukasser, A. Huttenhofer, and P. F. Stadler. Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat Biotechnol, 23(11):1383-1390, 2005.
32. W. W. Wasserman, M. Palumbo, W. Thompson, J. W. Fickett, and C. E. Lawrence. Human-mouse genome comparisons to locate regulatory sites. Nat Genet, 26(2):225-228, 2000.
33. S. Whelan, P. I. W. de Bakker, E. Quevillon, N. Rodriguez, and N. Goldman. PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. Nuc. Ac. Res., 34:D327-D331, 2006.
34. J. Wuyts, G. Perriere, and Y. Van De Peer. The european ribosomal RNA database. Nuc. Ac. Res., 32:D101-D103, 2004.
35. R.-F. Yeh, L. P. Lim, and C. B. Burge. Computational Inference of Homologous Gene Structures in the Human Genome. Gen. Res., 11(5):803-816, 2001.