Imagene: An integrated computer environment for sequence annotation and analysis

Bioinformatics

Volumn 15, Issue 1, 1999, Pages 2-15

  Médigue, Claudine ^a,b   Rechenmann, François ^c   Danchin, Antoine ^a   Viari, Alain ^b  

^a INSTITUT PASTEUR   (France)

^b SORBONNE UNIVERSITÉ   (France)

^c INRIA RHÔNE ALPES   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOMATION; COMPACT DISK; COMPUTER; COMPUTER PROGRAM; INFORMATION PROCESSING; METHODOLOGY; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

EID: 0342588237     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/15.1.2     Document Type: Article

References (36)

1. Altschul, S.F. and Gish, W. (1996) Local alignment statistics. Methods Enzymol., 266, 460-480.
2. Altschul, S.F. Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-110.
3. 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.
4. d'Aubenton Carafa, Y., Brody, E. and Thermes, C. (1990) Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures. J. Mol. Biol., 216, 835-858.
5. Bailey, L.C., Jr, Fischer, S., Schug, J., Crabtree, J., Gibson, M. and Overton, G.C. (1998) GAIA: framework annotation of genomic sequence. Genome Res., 8, 234-250.
6. Billoud, B., Kontic, M. and Viari, A. (1996) Palingol: a declarative programming language to describe nucleic acids' secondary structures and to scan sequence database. Nucleic Acids Res., 24, 1395-1403.
7. Bisson, G. and Garreau, A. (1995) APIC - a generic interface for sequencing projects. In Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 57-65.
8. Borodovsky, M. and McIninch, J.D. (1993) GeneMark © - Parallel gene recognition for both DNA strands. Comput. Chem., 17, 123-133.
9. Borodovsky, M., McIninch, J.D., Koonin, E.V., Rudd, K.E., Médigue, C. and Danchin, A. (1995) Detection of new genes in the bacterial genome using Markov models for three gene classes. Nucleic Acids Res., 17, 3554-3562.
10. Casari, G., Ouzounis, C., Valencia, A. and Sander, C. (1996) GeneQuiz II - Automatic function assignment for genome sequence analysis. In 1st Annual Symposium on Biocomputing. World Scientific, Hawaii, pp. 707-709.
11. Durbin, R. and Thierry-Mieg, J. (1993) The ACeDB genome database: document, code and data available at http://probe.nalusda.gov:8000/acedocs.
12. El-Mabrouk, N. and Lisacek, F. (1996) Very fast identification of RNA motifs in genomic DNA. Application to tRNA search in the yeast genome. J. Mol. Biol., 261, 46-55.
13. Fichant, G.A. and Burks, C. (1991) Identifying potential tRNA genes in genomic DNA sequences. J. Mol. Biol., 220, 659-671.
14. Frishman, D. and Mewes, H. (1997) PEDANTic genome analysis. Trends Genet., 13, 415-416.
15. Gaasterland, T. and Sensen, C.W. (1996a) Magpie automated genome interpretation. Trends Genet., 12, 76-78.
16. Gaasterland, T. and Sensen, C.W. (1996b) Fully automated genome analysis that reflects user needs and preferences. A detailled introduction to the MAGPIE system architecture. Biochimie, 78, 302-310.
17. Glémet, E. and Codani, J.J. (1997) LASSAP, a LArge Scale Sequence compArison Package. Comput. Applic. Biosci., 13, 137-143.
18. Gribskov, M., McLachlan, A.D. and Eisenberg, D. (1987) Profile analysis: detection of distantly related proteins. Proc. Natl Acad. Sci. USA, 84, 4355-4358.
19. Harris, N.L. (1997) Genotator: a workbench for sequence annotation. Genome Res., 7, 754-762.
20. Ilog-Control (1997) ILOG CONTROLVersion 1.4 - Reference Manual. ILOG. Gentilly, http:// www.ilog.com.
21. Ilog-PowerClasses (1996) ILOG POWER CLASSES Version 1.3 - Reference Manual. ILOG. Gentilly, http://www.ilog.com.
22. Ilog-Talk© (1995) ILOG TALK© Version 3.13 - Language Reference Manual. ILOG. Gentilly, http://www.ilog.com.
23. Ilog-Views (1995) ILOG VIEWS Version 2.3 - Reference Manual. ILOG. Gentilly, http://www.ilog.com.
24. Karp, P.D., Riley, M., Paley, S.M., Pellegrini-Toole, A. and Krummenacker, M. (1998) EcoCyc: Encyclopedia of Escherichia coli gene and metabolism. Nucleic Acids Res., 26, 50-53.
25. Kunst, F. et al. (1997) The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature, 390, 249-256.
26. Lowe, T.M. and Eddy, S.R. (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964.
27. Lukashin, A.V. and Borodovsky, M. (1998) GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res., 26, 1107-1115.
28. Médigue, C., Vermat, T., Bisson, G., Viari, A. and Danchin, A. (1995a) Cooperative computer system for genome sequence analysis. In Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology. AAAI/MIT Press, Menlo Park, CA, pp. 249-258.
29. Médigue, C., Moszer, I., Viari, A. and Danchin, A. (1995b) Analysis of a B. subtilis genome fragment using a cooperative computer system prototype. Gene, 165, GC37-GC51.
30. Perrière, G. and Gautier, C. (1993) ColiGene - Object-centered representation for the study of E.coli gene expressivity by sequence analysis. Biochimie, 75, 415-422.
31. Ptitsyn, A.A. and Grigorovich, D.A. (1995) Object-oriented data handler for sequence analysis software development. Comput. Applic. Biosci., 11, 583-589.
32. Rechenmann, F. and Uvietta, P. (1991) Shirka - An object-centered knowledge base management system. In Artificial Intelligence in Numerical and Symbolic Simulation. ALÉAS, Lyon.
33. Salzberg, S.L., Delcher, AL., Kasif, S. and White, O. (1998) Microbial gene identification using interpolated Markov models. Nucleic Acids Res., 26, 544-548.
34. Scharf, M., Schneider, R., Casari, G., Bork, P., Valencia, A., Ouzounis, C. and Sander, C. (1994) GeneQuiz - A workbench for sequence analysis. In Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 348-353.
35. Shine, J. and Dalgarno, L. (1974) The 3-terminal sequences of Escherichia coli 16S ribosomal RNA complementary to nonsense triplets and ribosome binding sites. Proc. Natl Acad. Sci. USA, 71, 1342-1346.
36. Willamowski, J., Chevenet, F. and François, J.M. (1994) A developement shell for cooperative problem-solving environments. Math. Comput. Simul., 36, 361-379.