Correspondence discriminant analysis: A multivariate method for comparing classes of protein and nucleic acid sequences

Bioinformatics

Volumn 12, Issue 6, 1996, Pages 519-524

  Perriere, G ^a   Lobry, J R ^a   Thioulouse, J ^a  

^a LABORATOIRE DE BIOMÉTRIE ET BIOLOGIE EVOLUTIVE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; CELL MEMBRANE PROTEIN; CYTOPLASM PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BACILLUS SUBTILIS; CELLULAR DISTRIBUTION; COMPUTER PROGRAM; DISCRIMINANT ANALYSIS; ESCHERICHIA COLI; HAEMOPHILUS; HAEMOPHILUS INFLUENZAE; INTERNET; MULTIVARIATE ANALYSIS; MYCOPLASMA; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

AMINO ACID SEQUENCE; BACILLUS SUBTILIS; BACTERIAL PROTEINS; CODON; DISCRIMINANT ANALYSIS; DNA; DNA, BACTERIAL; ESCHERICHIA COLI; HAEMOPHILUS INFLUENZAE; MEMBRANE PROTEINS; MOLECULAR SEQUENCE DATA; MULTIVARIATE ANALYSIS; MYCOPLASMA; PROTEINS; SEQUENCE ANALYSIS, DNA; SOFTWARE; SPECIES SPECIFICITY;

EID: 0030472379     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/12.6.519     Document Type: Article

References (28)

1. Bairoch.A. and Apweiler.R. (1996) The SWISS-PROT protein sequence data bank and its new supplement TREMBL. Nucleic Acids Res., 24, 21-25.
2. Bernardi, G., Olofsson, B., Filipski, J., Zerial, M., Salinas, J., Cuny, G., Meunier-Rotival, M. and Rodier, F. (1985) The mosaic genome of warm-blooded vertebrates. Science, 228, 953-958.
3. Blattner.F.R., Burland.V., Plunkett, G., Sofla.H.J. and Daniels, D.L. (1993) Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes. Nucleic Acids Res., 21, 5408-5417.
4. Burland.V., Plunkett.G., Daniels.D.L. and Blattner.F.R. (1993) DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication. Gcnomics, 16,551-561.
5. Chessel, D. and Thioulouse, J. (1996) L'analysc discriminante des corre-spondances. Documentation Themalique ADE-4, Vol. 5, Section 6. Universite Claude Bernard-Lyon 1, Lyon.
6. Daniels.D.L., Plunkett.G., Burland.V. and Blattner.F.R. (1992) Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes. Science, 257, 771-778.
7. Engelman, D.M., Steitz.T.A. and Goldman.A. (1986) Identifying non-polar transbilayer helices in amino acid sequences of membrane proteins. Annu. Rev. Biophys. Biophys. Chem., 15, 321-353.
8. Fleischmann, R.D. et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science, W), 496-512.
9. Frantino.M.P., Chao.L., Riley.M.A. and Ochman.H. (1996) Asymme-tries generated by transcription-coupled repair in enterobacterial genes. Science, 272, 107-109.
10. Fraser, C.M. et al. (1995) The minimal gene complement of Mycoplasma genitalium. Science, 270, 397-403.
11. Iida.Y. (1988) Categorical discriminant analysis of 3'-splice site signals of raRNA precursors in higher eucaryote genes. J. Theor. Bioi, 135, 109— 118.
12. Kanehisa.M. (1988) A multivariate analysis method for discriminating protein secondary structural segments. Protein Eng., 2, 87-92.
13. KJein.P., ICanehisa.M. and DeLisi.C. (1984) Prediction of protein function from sequence properties discriminant analysis of a data base. Biochim. Biophys. Ada, 787, 221—226.
14. KJein.P., Kanehisa.M. and DeLisi, C. (1985) The detection and classification of membrane-spanning proteins. Biochim. Biophvs. Acta, 815, 468,476.
15. Lobry.J.R. (1995) Properties of a general model of DNA evolution under no-strand-bias conditions. /. Mol. Evol., 40, 326-330.
16. Lobry.J.R. (1996) Asymmetric substitution patterns in the two DNA strands of bacteria. Mol. Biol. Evol., 13, 660-665.
17. Lobry, I.R. and GautieT.C. (1994) Hydrophobicity, expressivity and aromaticity are the major trends of amino acid usage in 999 Escherichia coli chromosome-encoded genes. Nucleic Acids Res., 22, 3174-3180.
18. Nakai.K.. and Kanehisa.M. (1991) Expert system for predicting protein localization sites in gram-negative bacteria. Proteins, 11, 95—110.
19. Nakashima, H. and Nishikawa.K. (1994) Discrimination of intracellular and extracellular proteins using amino acid composition and residue-pair frequencies. J. Mol. Biol., 238, 54-61.
20. Nakata.K… Kanehisa, M. and DeLisi, C. (1985) Prediction of splice junctions in mRNA sequences. Nucleic Acids Res., 13, 5327-5340.
21. Perriere.G., Moszer.I. and Gojobori, T. (1996) NRSub: a non-redundant database for Bacillus subtilis. Nucleic Acids Res., 1A, 41-45.
22. Plunkett.G., Burland.V., Daniels.D.L. and Blattner.F.R. (1993) Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes. Nucleic Acids Res., 21, 3391-3398.
23. Schaaper.R.M., Dunn.R.L. and Glickman.B.W. (1987) Mechanisms of ultraviolet-induced mutation. Mutational spectra in the Escherichia coli lad gene for a wild-type and an excision-repair-deficient strain. J. Mol. Biol., 198, 187-202.
24. Sofia.H.J., Burland.V., Daniels.D.L., Plunkett.G. and Blattner.F.R. (1994) Analysis of the Escherichia coli genome. V. DNA sequence of the region from 76.0 to 81.5 minutes. Nucleic Acids Res., 22, 2576-2586.
25. 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.
26. Thioulouse, J. and Chevenet, F. (1996) NetMul, a World-Wide Web user interface for multivariate analysis software. Compul. Slat. Data Anal., 21, 369-372.
27. Thioulousc, J., Doledec, S., Chessel, D. and Olivier, J.M. (1995) ADE software multivariate analysis and graphical display of environmental data. In Guariso, G. and Rizzoli, A. (eds). Software per I'Ambiente. Patron, Bolorua, pp. 57-62.
28. Yura.T., Mori.H., Nagai.H., Nagata.T., Ishihama.A., Fujita.N., Isono.K., Mizobuchi.K. and Nakata.A. (1992) Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region. Nucleic Acids Res., 20, 3305-3308.