Assessing protein coding region integrity in cDNA sequencing projects

Bioinformatics

Volumn 14, Issue 5, 1998, Pages 384-390

  Salamov, A A ^a   Nishikawa, T ^a   Swindells, M B ^a  

^a Helix Research Institute Inc   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA;

ARTICLE; COMPUTER PROGRAM; DISCRIMINANT ANALYSIS; DNA LIBRARY; DNA SEQUENCE; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; START CODON;

EID: 0031855858     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/14.5.384     Document Type: Article

References (21)

1. Adams, M.D. et al. (1991) Complementary DNA sequencing: Expressed Sequence Tags and the human genome project. Science, 252, 1651-1656.
2. Adams, M.D., Kerlavage, A.R., Fleischmann, R.D., Fuldner, R.A., Bult, C.J., Lee, N.H. and Kirkness, E.F. (1995) Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature, 377(Suppl.), 3-174.
3. Afifi, A.A. and Azen, S.P. (1979) Statistical Analysis. A Computer Oriented Approach. Academic Press, New York.
4. Barker, S. (1996) Japanese genomics combines state and industry backing. Nature, 380, 375.
5. Burge, C. and Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78-94.
6. Burset, M. and Guigo, R. (1996) Evaluation of gene structure prediction programs. Genomics, 34, 353-367.
7. Fleischmann, R.D. et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science, 269, 496-512.
8. Goffeau, A., Aert, R., Agostini-Carbone, L.M., Ahmed, A., Aigle, M., Alberghina, K. and Albermann, K. (1997) The Yeast Genome Directory. Nature, 387(Suppl.).
9. Gubler, U. and Hoffman, B.J. (1983) A simple and very efficient method for generating cDNA libraries. Gene, 25, 263-269.
10. Kozak, M. (1986) Point mutations define a sequence flanking the AUG initiation codon that modulates translation by eukaryotic ribosomes. Cell, 44, 283-292.
11. Kozak, M. (1996) Interpreting cDNA sequences: some insights from studies on translation. Mamm. Genome, 7, 563-574.
12. Kulp, D., Haussler, D., Reese, M.G. and Eeckman, F.H. (1996), A Generalized Hidden Markov Model for the Recognition of Human Genes in DNA, 4, 134-142, ISMB, AAAI/MIT Press.
13. Kyte, J. and Doolittle, R.F. (1982) A simple method for displaying the hydropathic character of a protein. J Mol. Biol , 157, 105-132.
14. Louis, B.G. and Ganoza, M.C. (1988) Signals determining translational start-site recognition in eukaryotes and their role in prediction of genetic reading frames. Mol. Biol. Rep., 13, 103-115.
15. Maruyama, K. and Sugano, S. (1994) Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligonucleotides. Gene, 138, 171-174.
16. McGeoch, D.J. (1985) On the predictive recognition of signal peptide sequences. Virus Res., 3, 271-286.
17. Myers, E.W. and Miller, W. (1988) Optimal alignments in linear space. Comput. Applic. Biosci , 4, 11-17.
18. Salamov, A.A. and Solovyev, V.V. (1997) Recognition of 3-processing sites of human mRNA precursors. Comput. Applic. Biosci., 13, 23-28.
19. Solovyev, V.V., Salamov, A.A. and Lawrence, C.B. (1994) Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames. Nucleic Acids Res., 22, 5156-5163.
20. Solovyev, V.V., Salamov, A.A. and Lawrence, C.B. (1995) Prediction of human gene structure using linear discriminant functions and dynamic programming. ISMB, 3, 367-375.
21. Zhang, M.Q. (1997) Identification of protein coding regions in the human genome by quadratic discriminant analysis. Proc Natl Acad. Sci. USA, 94, 565-568.