Back-translation for discovering distant protein homologies

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 5724 LNBI, Issue , 2009, Pages 108-120

  Gîrdea, Marta ^a   Noé, Laurent ^a   Kucherov, Gregory ^a  

^a INRIA   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ALIGNMENT; BIOINFORMATICS; DNA; DYNAMIC PROGRAMMING; EVOLUTIONARY ALGORITHMS; PROTEINS;

ALIGNMENT ALGORITHMS; ALIGNMENT METHODS; EVOLUTIONARY INFORMATION; EVOLUTIONARY PROCESS; FRAME-SHIFT MUTATION; GRAPH REPRESENTATION; PROTEIN ALIGNMENT; PROTEIN SEQUENCES;

DNA SEQUENCES;

EID: 70350398452     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-04241-6_10     Document Type: Conference Paper

References (24)

1. Raes, J., Van de Peer, Y.: Functional divergence of proteins through frameshift mutations. Trends in Genetics 21(8), 428-431 (2005)
2. Okamura, K., et al.: Frequent appearance of novel protein-coding sequences by frameshift translation. Genomics 88(6), 690-697 (2006)
3. Harrison, P., Yu, Z.: Frame disruptions in human mRNA transcripts, and their relationship with splicing and protein structures. BMC Genomics 8, 371 (2007)
4. Hahn, Y., Lee, B.: Identification of nine human-specific frameshift mutations by comparative analysis of the human and the chimpanzee genome sequences. Bioin-formatics 21(suppl. 1), i186-i194 (2005)
5. Grantham, R., Gautier, C., Gouy, M., Mercier, R., Pave, A.: Codon catalog usage and the genome hypothesis. Nucleic Acids Research (8), 49-62 (1980)
6. Shepherd, J.C.: Method to determine the reading frame of a protein from the purine/pyrimidine genome sequence and its possible evolutionary justification. Proceedings National Academy Sciences USA (78), 1596-1600 (1981)
7. Guigo, R.: DNA composition, codon usage and exon prediction. Nucleic Protein Databases, 53-80 (1999)
8. Leluk, J.: A new algorithm for analysis of the homology in protein primary structure. Computers and Chemistry 22(1), 123-131 (1998)
9. Leluk, J.: A non-statistical approach to protein mutational variability. BioSys-tems 56(2-3), 83-93 (2000)
10. Altschul, S., et al.: Basic local alignment search tool. JMB 215(3), 403-410 (1990)
11. Altschul, S., et al.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17), 3389-3402 (1997)
12. Pellegrini, M., Yeates, T.: Searching for Frameshift Evolutionary Relationships Between Protein Sequence Families. Proteins 37, 278-283 (1999)
13. Arvestad, L.: Aligning coding DNA in the presence of frame-shift errors. In: Hein, J., Apostolico, A. (eds.) CPM 1997. LNCS, vol. 1264, pp. 180-190. Springer, Heidelberg (1997)
14. Arvestad, L.: Algorithms for biological sequence alignment. PhD thesis, Royal Institute of Technology, Stocholm, Numerical Analysis and Computer Science (2000)
15. Blake, R., Hess, S., Nicholson-Tuell, J.: The influence of nearest neighbors on the rate and pattern of spontaneous point mutations. JME 34(3), 189-200 (1992)
16. Kosiol, C., Holmes, I., Goldman, N.: An Empirical Codon Model for Protein Sequence Evolution. Molecular Biology and Evolution 24(7), 1464 (2007)
17. Pedersen, A., Jensen, J.: A dependent-rates model and an MCMC-based methodology for the maximum-likelihood analysis of sequences with overlapping reading frames. Molecular Biology and Evolution 18, 763-776 (2001)
18. Lio, P., Goldman, N.: Models of Molecular Evolution and Phylogeny. Genome Research 8(12), 1233-1244 (1998)
19. Altschul, S., et al.: The estimation of statistical parameters for local alignment score distributions. Nucleic Acids Research 29(2), 351-361 (2001)
20. Olsen, R., Bundschuh, R., Hwa, T.: Rapid assessment of extremal statistics for gapped local alignment. In: ISMB, pp. 211-222 (1999)
21. Delaye, L., DeLuna, A., Lazcano, A., Becerra, A.: The origin of a novel gene through overprinting in Escherichia coli. BMC Evolutionary Biology 8, 31 (2008)
22. Hubbard, T., et al.: Ensembl 2007. Nucleic Acids Res. 35 (2007)
23. Clamp, M., et al.: Distinguishing protein-coding and noncoding genes in the human genome. Proc. Natl. Acad. Sci. 104(49), 19428-19433 (2007)
24. Oostra, B., Chiurazzi, P.: The fragile X gene and its function. Clinical genetics 60(6), 399 (2001)