Computational prediction of RNA editing sites

Bioinformatics

Volumn 20, Issue 17, 2004, Pages 3214-3220

  Bundschuh, R ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID DERIVATIVE; MESSENGER RNA;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; FUNGAL GENETICS; GENE SEQUENCE; GENETIC DIFFERENCE; MATHEMATICAL COMPUTING; MITOCHONDRION; NONHUMAN; PHYSARUM POLYCEPHALUM; PREDICTION; PRIORITY JOURNAL; RNA ANALYSIS; RNA EDITING; RNA SEQUENCE; STATISTICAL ANALYSIS;

CHONDROMYCES; MYXOGASTRIA; PHYSARUM; PHYSARUM POLYCEPHALUM;

EID: 10244259258     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth387     Document Type: Article

References (22)

1. Alberts,B., Johnson,A., Lewis,J., Raff,M., Roberts,K. and Walter,P. (1994) Molecular Biology of the Cell. Garland Publishing, New York.
2. Altschul,S.F., Madden,T.L., Schäffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
3. Brennicke,A., Marchfelder,A. and Binder,S. (1999) RNA editing. FEMS Microbiol. Rev., 23, 297-316.
4. Gish,W. and States,D.J. (1993) Identification of protein coding regions by database similarity search. Nat. Genet., 3, 266-272.
5. Gott,J.M., Visomirski,L.M. and Hunter,J.L. (1993) Substitutional and insertional RNA editing of the cytochrome c oxidase subunit 1 mRNA of Physarum polycephalum. J. Biol. Chem., 268, 25483-25486.
6. Gott,J.M. (2003) Expanding genome capacity via RNA editing. C.R. Biol., 326, 901-908.
7. Gray,M.W. (2003) Diversity and evolution of mitochondrial RNA editing systems. IUBMB Life, 55, 227-233.
8. Holmes,I. and Durbin,R. (1998) Dynamic programming alignment accuracy. In Istrail,S., Pevzner,P. and Waterman,M. (eds), Proceedings of the Seventh Annual International Conference on Computational Molecular Biology. ACM press, New York, pp. 102-108.
9. Horton,T.L. and Landweber,L.F. (2000) Evolution of four types of RNA editing in myxomycetes. RNA, 6, 1339-1346.
10. Hughey,R. and Krogh,A. (1996) Hidden Markov Models for sequence analysis: extension and analysis of the basic method. Comput. Appl. Biosci., 12, 95-107.
11. Karlin,S. and Altschul,S.F. (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl Acad. Sci. USA, 87, 264-2268.
12. Mahendran,R., Spottswood,M.R. and Miller,D.L. (1991) RNA editing by cytidine insertion in mitochondria of Physarum polycephalum. Nature, 349, 434-438.
13. Miller,D., Mahendran,R., Spottswood,M., Costandy,H., Wand,S., Ling,M.L. and Yang,N. (1993) Insertional editing in mitochondria of Physarum. Semin. Cell Biol., 4, 261-266.
14. Needleman,S.B. and Wunsch,C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
15. Robinson,A.B. and Robinson,L.R. (1991) Distribution of glutamine and asparagine residues and their near neighbors in peptides and proteins. Proc. Natl Acad. Sci. USA, 88, 8880-8884.
16. Smith,S.F. and Waterman,M.S. (1981) Comparison of biosequences. Adv. Appl. Math., 2, 482-489.
17. Smith,H.C., Gott,J.M. and Hanson,M.R. (1997) A guide to RNA editing. RNA, 3, 1105-1123.
18. Takano,H., Abe,T., Sakurai,R., Moriyama,Y., Miyazawa,Y., Nozaki,H., Kawano,S., Sasaki,N. and Kuroiwa,T. (2001) The complete DNA sequence of the mitochondrial genome of Physarum polycephalum. Mol. Gen. Genet., 264, 539-545.
19. Thorne,J.L., Kishino,H. and Felsenstein,J. (1991) An evolutionary model for maximum likelihood alignment of DNA sequences. J. Mol. Evol., 33, 114-124.
20. Wang,S.S., Mahendran,R. and Miller,D.L. (1999) Editing of cytochrome b mRNA in Physarum mitochondria. J. Biol. Chem., 274, 2725-2731.
21. Waterman,M.S. (1994) Introduction to Computational Biology Chapman and Hall, London.
22. Yu,Y.K. and Hwa,T. (2001). Statistical significance of probabilistic sequence alignment and related local hidden markov models. J. Comput. Biol., 8, 249-282.