Computational identification of protein coding potential of conserved sequence tags through cross-species evolutionary analysis

Nucleic Acids Research

Volumn 31, Issue 15, 2003, Pages 4639-4645

  Mignone, Flavio ^b   Grillo, Giorgio ^a   Liuni, Sabino ^a   Pesole, Graziano ^b  

^a CNR   (Italy)

^b UNIVERSITY OF MILAN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ALTERNATIVE RNA SPLICING; ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; EXON; GENETIC CODE; GENETIC CONSERVATION; HUMAN; HUMAN GENOME; MATHEMATICAL COMPUTING; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; SPECIES COMPARISON; UNINDEXED SEQUENCE; VALIDATION PROCESS; ANIMAL; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; GENETICS; GENOME; METHODOLOGY; MOLECULAR GENETICS; MOUSE; SEQUENCE HOMOLOGY; UNTRANSLATED REGION;

COMPLEMENTARY DNA; MESSENGER RNA; PROTEIN;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DNA, COMPLEMENTARY; EVOLUTION, MOLECULAR; EXONS; GENETIC CODE; GENOME; HUMANS; MICE; MOLECULAR SEQUENCE DATA; PROTEINS; RNA, MESSENGER; SEQUENCE HOMOLOGY, NUCLEIC ACID; SOFTWARE; UNTRANSLATED REGIONS;

EID: 0042161833     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg483     Document Type: Article

References (20)

1. Delcher,A.L., Harmon,D., Kasif,S., White,O. and Salzberg,S.L. (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res., 27, 4636-4641.
2. Besemer,J., Lomsadze,A. and Borodovsky,M. (2001) GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res., 29, 2607-2618.
3. Burge,C. and Karlin,S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78-94.
4. Krogh,A. (2000) Using database matches with for HMMGene for automated gene detection in Drosophila. Genome Res., 10, 523-528.
5. Rogic,S., Mackworth,A.K. and Ouellette,F.B. (2001) Evaluation of gene-finding programs on mammalian sequences. Genome Res., 11, 817-832.
6. Korf,I., Flicek,P., Duan,D. and Brent,M.R. (2001) Integrating genomic homology into gene structure prediction. Bioinformatics, 17 (suppl. 1), S140-S148.
7. Pachter,L., Alexandersson,M. and Cawley,S. (2002) Applications of generalized pair hidden Markov models to alignment and gene finding problems. J. Comput. Biol., 9, 389-399.
8. Makalowski,W. and Boguski,M.S. (1998) Evolutionary parameters of the transcribed mammalian genome: an analysis of 2,820 orthologous rodent and human sequences. Proc. Natl Acad. Sci. USA, 95, 9407-9412.
9. Pennacchio,L.A. and Rubin,E.M. (2001) Genomic strategies to identify mammalian regulatory sequences. Nature Rev. Genet., 2, 100-109.
10. Badger,J.H. and Olsen,G.J. (1999) CRITICA: coding region identification tool invoking comparative analysis. Mol. Biol. Evol., 16, 512-524.
11. Wiehe,T., Gebauer-Jung,S., Mitchell-Olds,T. and Guigo,R. (2001) SGP-1: prediction and validation of homologous genes based on sequence alignments. Genome Res., 11, 1574-1583.
12. Rivas,E. and Eddy,S.R. (2001) Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics, 2, 8.
13. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
14. Makalowski,W., Zhang,J. and Boguski,M. (1996) Comparative analysis of 1196 orthologous mouse and human full-length mRNA and protein sequences. Genome Res., 6, 846-857.
15. Jareborg,N., Birney,E. and Durbin,R. (1999) Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs. Genome Res., 9, 815-824.
16. Pesole,G., Liuni,S., Grillo,G., Licciulli,F., Mignone,F., Gissi,C. and Saccone,C. (2002) UTRdb and UTRsite: specialized databases of sequences and functional elements of 5′ and 3′ untranslated regions of eukaryotic mRNAs. Update 2002. Nucleic Acids Res., 30, 335-340.
17. Hubbard,T., Barker,D., Birney,E., Cameron,G., Chen,Y., Clark,L., Cox,T., Cuff,J., Curwen,V., Down,T. et al. (2002) The Ensembl genome database project. Nucleic Acids Res., 30, 38-41.
18. Collins,J.E., Goward,M.E., Cole,C.G., Smink,L.J., Huckle,E.J., Knowles,S., Bye,J.M., Beare,D.M. and Dunham,I. (2003) Reevaluating human gene annotation: a second-generation analysis of chromosome 22. Genome Res., 13, 27-36.
19. Dermitzakis,E.T., Reymond,A., Lyle,R., Scamuffa,N., Ucla,C., Deutsch,S., Stevenson,B.J., Flegel,V., Bucher,P., Jongeneel,C.V. et al. (2002) Numerous potentially functional but non-genic conserved sequences on human chromosome 21. Nature, 420, 578-582.
20. Dubchak,I., Brudno,M., Loots,G.G., Pachter,L., Mayor,C., Rubin,E.M. and Frazer,K.A. (2000) Active conservation of noncoding sequences revealed by three-way species comparisons. Genome Res., 10, 1304-1306.