Accès gratuit
Med Sci (Paris)
Volume 18, Numéro 2, Février 2002
Page(s) 237 - 250
Section Repères : Lexique
Publié en ligne 15 février 2002
  1. Stormo GD. Consensus patterns in DNA. Meth Enzymol 1990; 183 : 211–21.
  2. Sagot MF. Spelling approximate repeated or common motifs using a suffix tree. In : Lucchesi CL, Moura AV, eds. LATIN’98 : theoretical informatics lecture notes in computer science, vol. 1380. Berlin: Springer-Verlag, 1998 : 111–27.
  3. Bailey TL, Elkan C. ParaMEME, a parallel implementation and a web interface for a DNA and protein motif discovery tool. Comput Appl BIOSci 1996; 12 : 303–10.
  4. Reinert G, Schbath S, Waterman MS. Probabilistic and statistical properties of words: an overview. J Comput Biol 2000; 7 : 1–46.
  5. d’Aubenton Carafa Y, Brody E, Thermes C. Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures. J Mol Biol 1990; 216 : 835–58.
  6. Prestridge DS. Predicting Pol II promoter sequence using transcription factor binding sites. J Mol Biol 1995; 249 : 923–32.
  7. Tolstrup N, Rouzé P, Brunak S. A branch point consensus from Arabidopsis found by non circular analysis allows for better prediction of acceptor sites. Nucleic Acids Res 1997; 25 : 3159–63.
  8. Brendel V, Kleffe J, Carle Urioste JC, Walbot V. Prediction of splice sites in plant pre-mRNA from sequence properties. J Mol Biol 1998; 276 : 85–104.
  9. Pedersen AG, Nielsen H. Neutral network prediction of translation initiation sites in eukaryotes: perspectives for EST and genome analysis. In : Gaasterland T, Karp P, Karplus K, Ouzounis C, Sander C, Valencia A, eds. The fifth international conference on intelligent systems for molecular biology. Halkidiki ,Greece: AAAI/MIT Press, 1997 : 226–33.
  10. Borodovsky M, McIninch JD. GeneMark : parallel gene recognition for both DNA strands. Comp Chem 1993; 17 : 123–33.
  11. Salzberg SL, Delcher AL, Kasif S, White O. Microbial gene identification using interpolated Markov models. Nucleic Acids Res 1998; 26 : 544–8.
  12. Burge C, Karlin S. Prediction of complete gene structure in human genomic DNA. J Mol Biol 1998; 268 : 78–94.
  13. Salzberg SL, Pertea M., Delcher AL, Gardner MJ, Tettelin H. Interpolated Markov models for eucaryotic gene finding. Genomic 1999; 59 : 24–31.
  14. Snyder EE, Stormo GD. Identification of protein coding regions in genomic DNA. J Mol Biol 1998; 248 : 1–18.
  15. Salzberg SL, Delcher AL, Fasman K, Henderson J. A decision tree system for finding genes in DNA. J Comput Biol 1998; 5 : 667–80.
  16. Lukashin AV, Borodovsky M. GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res 1998; 26 : 1107–15.
  17. Krogh A. Two methods for improving performance of a HMM and their application for gene finding. In : Gaasterland T, Karp P, Karplus K, Ouzounis C, Sander C, Valencia A eds. The fifth international conference on intelligent systems for molecular biology. Halkidiki Greece: AAAI/MIT Press, 1997 : 179–86.
  18. Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res 1998; 8 : 967–74.
  19. Jiang J, Jacob HJ. EbEST: an automated tool using expressed sequence tags to delineate gene structure. Genome Res 1998; 8 : 268–75.
  20. Bairoch A, Apweiler R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 2000; 28 : 45–8.
  21. Bocs S, Danchin A, Médigue C. Re-annotation of genomes microbial CoDing Sequences : finding new genes and inaccurately annotated genes. BMC BioInformatics 2002 (sous presse).
  22. Borodovsky M, McIninch J, Médigue C, Rudd K, Danchin A. Detection of new genes in the bacterial genome using Markov models for three gene classes. Nucleic Acids Res 1995; 17 : 3554–62.
  23. Guédon Y. Computational methods for discrete hidden semi-Markov chains. Appl Stochastic Models Business Industry 1999; 15 : 195–224.
  24. Bork P. Powers and pitfalls in sequence analysis: the 70% hurdle. Genome Res 2000; 10 : 398–400.
  25. Pavy N, Rombauts S, Dehais P, et al. Evaluation of gene prediction software using a genomic data set : application to Arabidopsis thaliana sequences. Bioinformatics 1999; 15 : 887–99.
  26. Lander ES, Linton LM, Birren B, et al. Initial sequencing and analysis of the human genome. Nature 2001; 409 : 860–921.
  27. Altschul SF, Madden TL, Schäffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25 : 3389–402.
  28. Hofmann K, Bucher P, Falquet L, Bairoch A. The PROSITE database, its status in 1999. Nucleic Acids Res 1999; 27 : 215–9.
  29. Bateman A, Birney E, Durbin R, Eddy SR, Howe KL, Sonnhammer ELL. The Pfam protein families database. Nucleic Acids Res 2000; 28 : 263–6.
  30. Brazma A. On the importance of standardisation in life sciences. Bioinformatics 2001; 17 : 113–4.
  31. Berman HM, Westbrook J, Feng Z, et al. The protein data bank. Nucleic Acids Res 2000; 28 : 235–42.
  32. Nitschké P, Guerdoux-Jamet P, Chiapello H, et al. Indigo: a world-wide-web review on genomes and gene functions. FEMS Microbiol Rev 1998; 22 : 207–27.
  33. Salgado H, Santos A, Garza-Ramos U, van Helden J, Diaz E, Collados-Vides J. RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli. Nucleic Acids Res 1999; 27 : 59–60.
  34. Wingender E, Chen X, Fricke E, et al. The TRANSFAC system on gene expression regulation. Nucleic Acids Res 2001; 29 : 281–3.
  35. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000; 28 : 33–6.
  36. Overbeek R, Larsen L, Maltsev N, Pusch GD, Selkov E. WIT: a system for metabolic reconstructions and comparative analysis of the genomes. In : Letovsky C, Kluwer S, eds. Mol Biol Databases 2002 (sous presse).
  37. Riley M, Labedan B. Protein evolution viewed through Escherichia coli protein sequences: introducing the notion of structural segment of homology, the module. J Mol Biol 1997; 269 : 1–12.
  38. Perrière G, Duret L, Gouy M. HOBACGEN: database system for comparative genomics in bacteria. Genome Res 2000; 10 : 379–85.
  39. Overbeek R, Fonstein M, D’Souza M, Pusch GD, Maltsev N. The use of gene clusters to infer functional coupling. Proc Natl Acad Sci USA 1999; 96 : 2896–901.
  40. Snel B, Lehmann G, Bork P, Huynen MA. STRING: a webserver to retrieve and display the repeatedly occuring neighbourhood of a gene. Nucleic Acids Res 2000; 28 : 3442–4.
  41. Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000; 28 : 29–34.
  42. Karp PD. Integrated access to metabolic and genomic data. J Comp Biol 1996; 3 : 191–212.
  43. Gaasterland T, Sensen CW. Fully automated genome analysis that reflects user needs and preferences. A detailled introduction to the MAGPIE system architecture. Biochimie 1996; 78 : 302–10.
  44. Frishman D, Albermann K, Hani J, et al. Functional and structural genomics using PEDANT. Bioinformatics 2001; 17 : 44–57.
  45. Andrade M, Brown N, Leroy C, et al. Automated genome sequence analysis and annotation. Bioinformatics 1999; 15 : 391–412.
  46. Bailey LC, Fischer S, Schug J, Crabtree J, Gibson M, Overton GC. GAIA: framework annotation of genomic sequence. Genome Res 1998; 8 : 234–50.
  47. Walker DR, Koonin EV. SEALS: a system for easy analysis of lots of sequences. In: Menlo Park A, ed. Proceedings of the international conference on intelligent systems for molecular biology. Halkidiki, Greece: AAAI/MIT Press, 1997 : 333–9.
  48. Harris NL. Genotator: a workbench for sequence annotation. Genome Res 1997; 7 : 754–62.
  49. Médigue C, Rechenmann F, Danchin A, Viari A. Imagene : an integrated computer environment for sequence annotation and analysis. Bioinformatics 1999; 15 : 2–15.
  50. Rutherford J, Parkhill J, Crook T, et al. Artemis: sequence visualisation and annotation. Bioinformatics 2000; 16 : 944–5.
  51. Galperin MY, Koonin EV. Sources of systematic error in functional annotation of genomes : domain rearrangement, non-orthologous gene displacement, and operon disruption. In Silico Biol 1998; 1 : 0007.
  52. Fitch W. Distinguishing homologous from analogous protein. Syst Zool 1970; 19 : 99–113.
  53. Fitch W. Homology a personal view on some of the problem. Trends Genet 2000; 16 : 2277–23.

Current usage metrics show cumulative count of Article Views (full-text article views including HTML views, PDF and ePub downloads, according to the available data) and Abstracts Views on Vision4Press platform.

Data correspond to usage on the plateform after 2015. The current usage metrics is available 48-96 hours after online publication and is updated daily on week days.

Initial download of the metrics may take a while.