AGMIAL: Implementing an annotation strategy for prokaryote genomes as a distributed system

Nucleic Acids Research

Volumn 34, Issue 12, 2006, Pages 3533-3545

  Bryson, K ^a,c   Loux, V ^a   Bossy, R ^a   Nicolas, P ^a   Chaillou, S ^b   Van De Guchte, M ^b   Penaud, S ^b   Maguin, E ^b   Hoebeke, M ^a,d   Bessieres P ^a   Gibrat, J F ^a  

^a INRA Institut National de la Recherche Agronomique   (France)

^b CEMAGREF   (France)

^c UNIVERSITY COLLEGE LONDON   (United Kingdom)

^d UNIVERSITÉ D EVRY VAL D ESSONNE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN;

ARTICLE; BACTERIAL GENOME; BIOLOGY; COMPUTER INTERFACE; COMPUTER PROGRAM; GENETICS; GENOME; GENOMICS; INTERNET;

BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; GENOME, ARCHAEAL; GENOME, BACTERIAL; GENOMICS; INTERNET; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 33746809569     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl471     Document Type: Review

References (72)

1. Kunst,F., Ogasawara,N., Moszer,I., Albertini,A.M., Alloni,G., Azevedo,V., Bertero,M.G., Bessieres,P. et al. (1997) The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature, 390, 249-256. (Pubitemid 27513299)
2. Stein,L. (2001) Genome annotation: from sequence to biology. Nature Rev. Genet., 2, 493-503.
3. Kitano,H. (2002) Systems biology: a brief overview. Science, 295, 1662-1664.
4. Bork,P., Dandekar,T., Diaz-Lazcoz,Y., Eisenhaber,F., Huynen,M. and Yuan,Y. (1998) Predicting function: from genes to genomes and back. J. Mol. Biol., 283, 707-725. (Pubitemid 28495340)
5. Jefery,C.J. (2000) Moonlighting proteins. Trends Biochem. Sci., 24, 8-11.
6. Riley,M. (1997) Genes and proteins in Escherichia coli k-12 (GenProtEC). Nucleic Acids Res., 25, 51-52.
7. Galperin,M.Y. and Koonin,E.V. (1998) Sources of systematic error in functional annotation of genomes: domain rearrangement, nonorthologous gene displacement and operon disruption. In Silico Biol., 1, 55-67.
8. Letunic,I., Copley,R.R., Schmidt,S., Ciccarelli,F.D., Doerks,T., Schultz,J., Ponting,C.P. and Bork,P. (2004) SMART 4.0: towards genomic data integration. Nucleic. Acids. Res., 32, D142-D144. (Pubitemid 38081624)
9. 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.
10. Pearson,W.R. (2000) Flexible sequence similarity searching with the FASTA3 program package. Meth. Mol. Biol., 132, 185-219.
11. Altschul,S.F., Madden,T.L., Schaffer,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. (Pubitemid 27359211)
12. Bateman,A., Birney,E., Cerruti,L., Durbin,R., Etwiller,L., Eddy,S.R., Griffths-Jones,S., Howe,K.L., Marshall,M. and Sonnhammer,E.L. (2002) The Pfam protein families database. Nucleic Acids Res., 30, 276-280. (Pubitemid 34679563)
13. Falquet,L., Pagni,M., Bucher,P., Hulo,N., Sigrist,C.J., Hofmann,K. and Bairoch,A. (2002) The PROSITE database, its status in 2002. Nucleic Acids Res., 30, 235-238. (Pubitemid 34679552)
14. Marin,A., Pothier,J., Zimmermann,K. and Gibrat,J.-F. (2002) FROST: a filterbased fold recognition method. Proteins, 49, 493-509. (Pubitemid 35388135)
15. Notebaart,R.A., Huynen,M.A., Teusink,B., Siezen,R.J. and Snel,B. (2005) Correlation between sequence conservation and the genomic context after gene duplication. Nucleic Acids Res., 33, 6164-6171. (Pubitemid 41742554)
16. Huynen,M.A., Snel,B., Mering,C. and Bork,P. (2003) Function prediction and protein networks. Curr. Opin. Cell. Biol., 15, 191-198. (Pubitemid 36332194)
17. Gardy,J.L., Laird,M.R., Chen,F., Rey,S., Walsh,C.J., Ester,M. and Brinkman,F.S. (2005) PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics, 21, 617-623. (Pubitemid 40424787)
18. Riley,M. (1998) Systems for categorizing functions of gene products. Curr. Opin. Struct. Biol., 8, 388-392.
19. The Gene Ontology Consortium (2000) Gene Ontology: tool for the unification of biology. Nature. Genet., 25, 25-29.
20. Ruepp,A., Zollner,A., Maier,D., Albermann,K., Hani,J., Mokrejs,M., Tetko,I., Guldener,U., Mannhaupt,G., Munsterkotter,M. and Mewes,H.W. (2004) The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res., 32, 5539-5545. (Pubitemid 39545671)
21. Nicolas,P., Bize,L., Muri,F., Hoebeke,M., Rodolphe,F., Ehrlich,S.D., Prum,B. and Bessires,P. (2002) Mining Bacillus subtilis chromosome heterogeneities using Hidden Markov Models. Nucleic Acids Res., 30, 1418-1426. (Pubitemid 34679721)
22. 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. (Pubitemid 27298263)
23. d'Aubenton,C.Y., Brody,E. and Thermes,C. (1990) Prediction of rhoindependent Escherichia coli transcription terminators. a statistical analysis of their RNA stem-loop structures. J. Mol. Biol., 216, 835-858.
24. Rutherford,K., Parkhill,J., Crook,J., Horsnell,T., Rice,P., Rajandream,M.A. and Barrell,B. (2000) Artemis: sequence visualization and annotation. Bioinformatics., 16, 944-945.
25. Hoebeke,M., Nicolas,P. and Bessieres,P. (2003) MuGeN: simultaneous exploration of multiple genomes and computer analysis results. Bioinformatics, 19, 859-864. (Pubitemid 36582402)
26. Stothard,P. and Wishart,D.S. (2005) Circular genome visualization and exploration using CGView. Bioinformatics, 21, 537-539. (Pubitemid 40310241)
27. Wootton,J.C. (1994) Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput. Chem., 18, 269-285.
28. Jones,D.T., Taylor,W.R. and Thornton,J.M. (1994) A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry, 33, 3038-3049. (Pubitemid 24103366)
29. Lupas,A., Van Dyke,M. and Stock,J. (1991) Predicting coiled coils from protein sequences. Science, 252, 1162-1164. (Pubitemid 21917026)
30. von Heijne,G. (1986) A new method for predicting signal sequence cleavage sites. Nucleic Acids Res., 14, 4683-4690.
31. Zdobnov,E.M. and Apweiler,R. (1986) InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics, 17, 847-848.
32. Haft,D.H., Selengut,J.D. and White,O. (2003) The TIGRFAMs database of protein families. Nucleic Acids Res., 31, 371-373. (Pubitemid 36150405)
33. Bauer-Marchler,A., Anderson,J.B., Cherukuri,P.F., DeWeese-Scott,C., Geer,L.Y., Gwadz,M., He,S., Hurwitz,D.I., Jackson,J.D., Ke,Z. et al. (2005) CDD: a conserved domain database for protein classification. Nucleic Acids Res., 33, D192-D196. (Pubitemid 40207858)
34. Tatusov,R.L., Natale,D.A., Garkavtsev,I.V., Tatusova,T.A., Shankavaram,U.T., Rao,B.S., Kiryutin,B., Galperin,M.Y., Fedorova,N.D. and Koonin,E.V. (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res., 29, 22-28. (Pubitemid 32054398)
35. Clamp,M., Cuff,J., Searle,S.M. and Barton,G.J. (2004) The Jalview java alignment editor. Bioinformatics, 20, 426-427. (Pubitemid 38262778)
36. Attwood,T.K., Bradley,P., Flower,D.R., Gaulton,A., Maudling,N., Mitchell,A.L., Moulton,G., Nordle,A., Paine,K. and Taylor,P. (2003) PRINTS and its automatic supplement, prePRINTS. Nucleic Acids Res., 31, 400-402. (Pubitemid 36150412)
37. Kanehisa,M., Goto,S., Kawashima,S., Okuno,Y. and Hattori,M. (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res., 32, D277-D280. (Pubitemid 38081656)
38. Chaillou,S., Champomier-Vergs,M.-C., Cornet,M., Crutz-Le Coq,A.-M., Dudez,A.-M., Martin,V., Beaufils,S., Darbon-Rongre,E., Bossy,R. and Loux,V. (2005) The complete genome sequence of the meat-borne lactic acid bacterium Lactobacillus sakei 23k. Nat. Biotechnol., 23, 1527-1533. (Pubitemid 41752930)
39. van de Guchte,M., Penaud,S., Grimaldi,C., Barbe,V., Bryson,K., Nicolas,P., Robert,C., Oztas,S., Mangenot,S., Couloux,A. et al. (2006) The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution. Proc. Natl Acad. Sci., USA, 103, 9274-9279. (Pubitemid 43902568)
40. Gaasterland,T. and Sensen,C.W. (1996) Fully automated genome analysis that reflects user needs and preferences. a detailed introduction to the MAGPIE system architecture. Biochimie, 78, 302-310. (Pubitemid 26394637)
41. Harris,N.L. (1997) Genotator: a workbench for sequence annotation. Genome Res., 7, 754-762.
42. Bailey,L.C., Fischer,S., Schug,J., Crabtree,J., Gibson,M. and Overton,G.C. (1998) GAIA: framework annotation of genomic sequence. Genome Res., 8, 234-250. (Pubitemid 28177235)
43. Medigue,C., Rechenmann,F., Danchin,A. and Viari,A. (1999) Imagene: an integrated computer environment for sequence annotation and analysis. Bioinformatics, 15, 2-15. (Pubitemid 29101195)
44. Andrade,M.A., Brown,N.P., Leroy,C., Hoersch,S., de Daruvar,A., Reich,C., Franchini,A., Tamames,J., Valencia,A. and Ouzounis,C. (1999) Automated genome sequence analysis and annotation. Bioinformatics, 15, 391-412. (Pubitemid 29312628)
45. Decker,K., Zheng,X. and Schmidt,C. (2001) A multi-agent system for automated genomic annotation. In Proceedings of the fifth international conference on Autonomous agents, 433-440, ACM Press.
46. Frishman,D., Albermann,K., Hani,J., Heumann,K., Metanomski,A., Zollner,A. and Mewes,H.W. (2001) Functional and structural genomics using PEDANT. Bioinformatics, 17, 44-57. (Pubitemid 32178012)
47. Hubbard,T., Barker,D., Birney,E., Cameron,G., Chen,L., Clark,Y., Cox,T., Cu,J., Curwen,V. and Down,T. (2002) The ENSEMBL genome database project. Nucleic Acids Res., 30, 38-41. (Pubitemid 34679498)
48. Lewis,S.E., Searle,S.M., Harris,N., Gibson,M., Lyer,V., Richter,J., Wiel,C., Bayraktaroglir,L., Birney,E. and Crosby,M.A. (2002) Apollo: a sequence annotation editor. Genome Biol., 3, 1-14.
49. Searle,S.M., Gilbert,J., Iyer,V. and Clamp,M. (2004) The OTTER annotation system. Genome Res., 14, 963-970. (Pubitemid 38660517)
50. Sakata,K., Nagamura,Y., Numa,H., Antonio,B.A., Nagasaki,H., Idonuma,A., Watanabe,W., Shimizu,Y., Horiuchi,I., Matsumoto,T., Sasaki,T. and Higo,K. (2002) RiceGAAS: an automated annotation system and database for rice genome sequence. Nucleic Acids Res., 30, 98-102. (Pubitemid 34679515)
51. Wilkinson,M.D., Block,D. and Crosby,W.L. (2002) Genquire: genome annotation browser/editor. Bioinformatics, 18, 1398-1399. (Pubitemid 35244199)
52. Bazzan,A.L.C., Duarte,R., Pitinga,A.N., Schroeder,L.F., Souto,F.D.A. and Ceroni da Silva,S. (2003) ATUGC-an agent-based environment for automatic annotation of genomes. International Journal of Cooperative Information Systems, 12, 241-273. (Pubitemid 36500659)
53. Meyer,F., Goesmann,A., McHardy,A.C., Bartels,D., Bekel,T., Clausen,J., Kalinowski,J., Linke,B., Rupp,O. and Giegerich,R. (2003) GenDB-an open source genome annotation system for prokaryote genomes. Nucleic Acids Res., 31, 2187-2195. (Pubitemid 37442085)
54. Glasner,J.D., Liss,P., Plunkett,G., Darling,A., Prasad,T., Rusch,M., Byrnes,A., Gilson,M., Biehl,B. and Blattner,F.R. (2002) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res., 31, 147-151. (Pubitemid 36150353)
55. Almeida,L.G.P., Paixao,R., Souza,R.C., da Costa,G.C., Barrientos,F.J., dos Santos,M.T., de Almeida,D.F. and Vasconcelos,A.T.R. (2004) A system for automated bacterial (genome) integrated annotation-SABIA. Bioinformatics, 20, 2832-2833. (Pubitemid 39530171)
56. Vallenet,D., Labarre,L., Rouy,Z., Barbe,V., Bocs,S., Cruveiller,S., Lajus,A., Pascal,G., Scarpelli,C. and Medigue,C. (2006) MaGe: a microbial genome annotation system supported by synteny results. Nucleic Acids Res., 34, 53-65. (Pubitemid 43167917)
57. Gattiker,A., Gasteiger,E. and Bairoch,A. (2002) ScanProsite: a reference implementation of a PROSITE scanning tool. Appl. Bioinformatics, 1, 107-108.
58. Sigrist,C.J.A., Cerutti,L., Hulo,N., Gattiker,A., Falquet,L., Pagni,M., Bairoch,A. and Bucher,P. (2002) PROSITE: a documented data base using patterns and profiles as motif descriptors. Brief Bioinform, 3, 265-274.
59. Scordis,P., Flower,D.R. and Attwood,T.K. (1999) FingerPRINTScan: intelligent searching of the PRINTS motif database. Bioinformatics, 15, 799-806. (Pubitemid 30055194)
60. Wu,C.H., Nikolskaya,A., Huang,H., Yeh,L.S., Natale,D.A., Vinayaka,C.R., Hu,Z.Z., Mazumder,R., Kumar,S. and Kourtesis,P. (2004) PIRSF: family classification system at the Protein Information Resource. Nucleic Acids Res., 32, D112-D114. (Pubitemid 38081616)
61. Mi,H., Lazareva-Ulitsky,B., Loo,R., Kejariwal,A., Vandergri,J., Rabkin,S., Guo,N., Muruganujan,A., Doremieux,O. and Campbell,M.J. (2005) The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res., 33, D284-D288. (Pubitemid 40207879)
62. Gough,J., Karplus,K., Hughey,R. and Chothia,C. (2001) Assignment of homology to genome sequences using a library of Hidden Markov Models that represent all proteins of known structure. J. Mol. Biol., 313, 903-919. (Pubitemid 33063435)
63. Lee,D., Grant,A., Marsden,R.L. and Orengo,C. (2005) Identification and distribution of protein families in 120 completed genomes using Gene3D. Proteins, 59, 603-615. (Pubitemid 40594303)
64. Bru,C., Courcelle,E., Carrere,S., Beausse,Y., Dalmar,S. and Kahn,D. (2005) The ProDom database of protein domain families: more emphasis on 3d. Nucleic Acids Res., 33, D212-D215. (Pubitemid 40207862)
65. Dyrlov Bendtsen,J., Nielsen,H., von Heijne,G. and Brunak,S. (2004) Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol., 340, 783-795. (Pubitemid 38829638)
66. Moller,S., Croning,M.D.R. and Apweiler,R. (2001) Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics, 17, 646-653. (Pubitemid 32707587)
67. Bairoch,A., Apweiler,R., Wu,C.H., Barker,W.C., Boeckmann,B., Ferro,S., Gasteiger,E., Huang,H., Lopez,R. and Magrane,M. (2005) The universal protein resource (UniProt). Nucleic Acids Res., 33, D154-D159. (Pubitemid 40207850)
68. Deshpande,N., Addess,K.J., Bluhm,W.F., Merino-Ott,J.C., Townsend-Merino,W., Zhang,Q., Knezevich,C., Xie,L., Chen,L. and Feng,L. (2005) The RCSB protein data bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res., 33, D233-D237. (Pubitemid 40207868)
69. Andreeva,A., Howorth,D., Brenner,S.E., Hubbard,T.J., Chothia,C. and Murzin,A.G. (2004) SCOP database in 2004: re.nements integrate structure and sequence family data. Nucleic Acids. Res., 32, D226-D229. (Pubitemid 38081644)
70. Hulo,N., Sigrist,C.J., Le Saux,V., Langendijk-Genevaux,P.S., Bordoli,L., Gattiker,A., De Castro,E., Bucher,P. and Bairoch,A. (2004) Recent improvements to the PROSITE database. Nucleic Acids Res., 32, D134-D137. (Pubitemid 38081622)
71. Bateman,A., Coin,L., Durbin,R., Finn,R.D., Hollich,V., Griffiths,J., Khanna,A., Marshall,M., Moxon,S. and Sonnhammer,E.L. (2004) The Pfam protein families database. Nucleic Acids Res., 32, D138-D141. (Pubitemid 38081623)
72. Haft,D.H., Selengut,J.D. and White,O. (2003) The TIGRFAMs database of protein families. Nucleic Acids Res., 31, 371-337.