| Auteurs |
Titre |
Référence |
Thématique |
Type apprentissage |
Restrictions |
Plate-forme annotation |
| Abascal F., Valencia A. |
Automatic annotation of protein function based on family identification |
Proteins 2003, 53:683-692. |
Annotation |
|
|
|
| Al-Shahrour F., Arbiza L., Dopazo H., Huerta-Cepas J., Minguez P., Dopazo J. |
From genes to functional classes in the study of biological systems |
BMC Bioinformatics 2007, 8:114 |
Annotation |
|
|
FatScan |
| Andrade MA, Brown NP, Leroy C, Hoersch S, de Daruvar A, Reich C, Franchini A, Tamames J, Valencia A, Ouzounis C, Sander C. |
Automated genome sequence analysis and annotation |
Bioinformatics 1999, 15(5), 391-412. |
Annotation |
|
|
GeneQuiz |
| Arakaki AK, Tian W, Skolnick J. |
High precision multi-genome scale reannotation of enzyme function by EFICAz. |
BMC Genomics. 2006 Dec 13;7:315. |
Annotation |
Inférence, HMM |
Enzymes uniquement (Archae, Bacteries, Eucaryotes) |
|
| Bailey LC Jr, Fischer S, Schug J, Crabtree J, Gibson M, Overton GC. |
GAIA: Framework Annotation of Genomic Sequence |
Genome Research 1998, 8, 234-250 |
Annotation |
|
|
|
| Barutcuoglu Z, Schapire RE, Troyanskaya OG. |
Hierarchical multi-label prediction of gene function. |
Bioinformatics. 2006 Apr 1;22(7):830-6. Epub 2006 Jan 12. |
Annotation |
|
|
|
| Bazzan AL, Engel PM, Schroeder LF, da Silva SC. |
Automated annotation of Keywords for Proteins Related to Mycoplsmataceae Using Machine Learning Techniques |
Bioinformatics 2002, 18(S2) S35-S43 |
Annotation |
Multiagents et C4.5 Weka |
Mycoplasmataceae |
|
| Bellgard MI, Hiew HL, Hunter A, Wiebrands M. |
ORBIT: an integrated environment for user-customized bioinformatics tools. |
Bioinformatics. 1999 Oct;15(10):847-51. |
Annotation |
Plate-forme client-serveur qui peut être adaptée par l'utilisateur |
|
ORBIT |
| Biswas M, O'Rourke JF, Camon E, Fraser G, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva E, Mittard V, Mulder N, Phan I, Servant F, Apweiler R. |
Applications of InterPro in proteins annotation and genome analysis |
Brief Bioinformatics 2002, 3(3), 285-295. |
Annotation |
À base de règles |
|
RuleBase |
| Bradshaw C, Surendranath V, Habermann B |
ProFat: a web-absed tool for the functional annotation of protein sequences |
BMC Bioingormatics 2006, 7:466 |
Annotation |
text mining |
|
|
| Bryson K, Loux V, Bossy R, Nicolas P, Chaillou S, van de Guchte M, Penaud S, Maguin E, Hoebeke M, Bessieres P, Gibrat JF. |
AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. |
Nucleic Acids Res. 2006 Jul 19;34(12):3533-45. Print 2006. |
Annotation |
Non |
Procaryotes |
AGMIAL : interface d'accès à plusieurs analyses sur le génome complet (CAM) et chaque proteine (PAM). Lien avec DB Kegg (PAREO). Comparaison plusieurs génomes possible. |
| Cai Z, Mao X, Li S, Wei L. |
Genome comparison using Gene Ontology (GO) with statistical testing. |
BMC Bioinformatics. 2006 Aug 11;7:374. |
Annotation |
|
Analyse statistique de la comparaison de la répartition GO des gènes de 2 génomes (nombre de gènes différents) |
|
| Clare A, Karwath A, Ougham H, King RD. |
Functional bioinformatics for Arabidopsis thaliana. |
Bioinformatics. 2006 May 1;22(9):1130-6. Epub 2006 Feb 15. Erratum in: Bioinformatics. 2006 Jul 1;22(13):1674. |
Annotation |
|
A.thaliana |
|
| Datta S, Datta S. |
Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes. |
BMC Bioinformatics. 2006 Aug 31;7:397. |
Expression |
|
Gene expression |
|
| Descorps-Declere S, Ziebelin D, Rechenmann F, Viari A. |
Genepi: a blackboard framework for genome annotation. |
BMC Bioinformatics. 2006 Oct 12;7:450. |
Annotation |
|
|
Genepi |
| Devos D, Valencia A. |
Intrinsic errors in genome annotation. |
Trends Genet. 2001 Aug;17(8):429-31. |
Annotation Erreurs |
Non |
Estimation du taux d'erreur dans les annotations |
|
| Djebali S, Delaplace F, Crollius HR. |
Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA. |
Genome Biol. 2006;7 Suppl 1:S7.1-10. Epub 2006 Aug 7. |
Annotation |
Non : Utilise une réduction de DAG pour associer les exons de différents transcripts |
Eucaryotes |
Annotation structurale |
| Dolan ME, Holden CC, Beard MK, Bult CJ. |
Genomes as geography: using GIS technology to build interactive genome feature maps. |
BMC Bioinformatics. 2006 Sep 19;7:416. |
Visualisation |
|
|
|
| Duan ZH, Hughes B, Reichel L, Perez DM, Shi T. |
The relationship between protein sequences and their gene ontology functions. |
BMC Bioinformatics. 2006 Dec 12;7 Suppl 4:S11. |
Annotation |
Non |
|
|
| Enault F., Suhre K. and Claverie JM |
Phydbac "gene Function Predictor": a gene annotation tool based on genomic contexte analysis |
BMC Bioinformatics 2005, 6:247 |
Annotation |
|
E. coli |
PhydBac |
| Engelhardt B., Jordan M., Muratore K., and Brenner S. |
Protein Molecular Function Prediction by Bayesian Phylogenomics |
PLoS Comput Biol 2005, 1(5): e45 |
Annotation |
inférence statistique |
|
SIFTER (Statistical Inference of Function Through Evolutionary Relationships) |
| Fleischmann, W., Möller, S., Gateau, A., and Apweiler |
A novel method for automatic functional annotation of proteins |
Bioinformatics, 1999, 15, 228-233 |
Annotation |
|
|
|
| Friedberg I. |
Automated protein function prediction--the genomic challenge |
Brief Bioinform, 2006; 7(3): 225 - 242. |
Annotation |
|
|
|
| Frishman D, Mokrejs M, Kosykh D, Kastenmüller G, Kolesov G, Zubrzycki I, Gruber C, Geier B, Kaps A, Albermann K, Volz A, Wagner C, Fellenberg M, Heumann K, Mewes HW. |
The PEDANT genome database |
Nucleic Acids Research, 2003, Vol. 31, N°1, 207-211 |
Annotation |
|
|
|
| Gaasterland and Sensen |
Fully Automated Genome Analysis that reflects User Needs and preferences - a detailed Introduction to the MAGPIE System Architecture |
Biochimie 1996, 78(5), 302-310. |
Annotation |
|
|
|
| Gattiker A, Michoud K, Rivoire C, Auchincloss AH, Coudert E, Lima T, Kersey P, Pagni M, Sigrist CJ, Lachaize C, Veuthey AL, Gasteiger E, Bairoch A. |
Automated annotation of microbial proteomes in SWISS-PROT. |
Comput Biol Chem. 2003 Feb;27(1):49-58. |
Annotation |
Symbolique : règles concernant les familles de protéine avec des choix (par ex. selon le règne) |
Annotation automatique : uniquement les très bons hits blast (plutôt qu'une couverture complète) + ORFans (seq. sans similarité) ; archae + bacteria + plastid ; pour les eukaryotes : juste des suggetions car annotation trop complexe pour être automatisée |
HAMAP |
| Gilks WR, Audit B., De Angelis D., Tsoka S., Ouzounis CA |
Modeling the percolation of annotation errors in a database of proteins sequences |
Bioinformatics 2002, 18:1641-1649. |
Annotation |
Modèle probabiliste dynamique |
|
|
| Philippe Gouret P, Vitiello V, Balandraud N, Gilles A, Pontarotti P, Danchin EG. |
FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform |
BMC Bioinformatics. 2005 Aug 5;6:198. |
Annotation |
|
|
FIGENIX |
| Hull D, Wolstencroft K, Stevens R, Goble C, Pocock MR, Li P, Oinn T. |
Taverna: a tool for building and running workflows of services. |
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W729-32. |
WorkFlow |
|
|
|
| Iliopoulos I, Tsoka S, Andrade MA, Enright AJ, Carroll M, Poullet P, Promponas V, Liakopoulos T, Palaios G, Pasquier C, Hamodrakas S, Tamames J, Yagnik AT, Tramontano A, Devos D, Blaschke C, Valencia A, Brett D, Martin D, Leroy C, Rigoutsos I, Sander C, Ouzounis CA. |
Evaluation of annotation strategies using an entire genome sequence. |
Bioinformatics. 2003 Apr 12;19(6):717-26. |
Annotation Erreurs |
Non |
|
Système de représentation des données : GATOS : Genome AnnoTatiOn Systems |
| Jones CE, Baumann U, Brown AL. |
Automated methods of predicting the function of biological sequences using GO and BLAST. |
BMC Bioinformatics. 2005 Nov 15;6:272. |
Annotation |
|
|
|
| Jones CE, Brown AL, Baumann U. |
Estimating the annotation error rate of curated GO database sequence annotations. |
BMC Bioinformatics. 2007 May 22;8(1):170 [Epub ahead of print] |
Annotation |
|
|
|
| Karaoz U, Murali TM, Letovsky S, Zheng Y, Ding C, Cantor CR, Kasif S. |
Whole-genome annotation by using evidence integration in functional-linkage networks. |
Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2888-93. Epub 2004 Feb 23. |
Annotation |
|
|
|
| Khatri P, Draghici S. |
Ontological analysis of gene expression data: current tools, limitations, and open problems. |
Bioinformatics. 2005 Sep 15;21(18):3587-95. Epub 2005 Jun 30. |
Expression, Ontologie |
|
|
|
| King RD, Wise PH, Clare A. |
Confirmation of data mining based predictions of protein function. |
Bioinformatics. 2004 May 1;20(7):1110-8. Epub 2004 Feb 5. |
Annotation |
|
|
|
| King RD, Karwath A, Clare A, Dehaspe L. |
The utility of different representations of protein sequence for predicting functional class |
Bioinformatics. 2001 May;17(5):445-54. |
Annotation |
warmr + arbres + combinaison de classifieurs |
E. coli |
|
| King RD, Karwath A, Clare A, Dehaspe L. |
Accurate prediction of protein functional class from sequence in the M. tuberculosis and E. coli genomes using data mining |
Yeast. 2000 Dec;17(4):283-93. |
Annotation |
|
S.cerevisiae |
|
| Koski LB, Gray MW, Lang BF, Burger G. |
AutoFACT: an automatic functional annotation and classification tool. |
BMC Bioinformatics. 2005 Jun 16;6:151. |
Annotation |
|
|
|
| Krebs WG, Bourne PE. |
Stastically Rigourous Automated Protein Annotation |
Bioinformatics 2004, 20:1066-1073. |
Annotation |
|
|
|
| Kretschmann E, Fleischmann W, Apweiler R. |
Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT |
Bioinformatics. 2001 Oct;17(10):920-6. |
Annotation |
|
|
Spearmint |
| Laskowski RA, Watson JD, Thornton JM. |
ProFunc: a server for predicting protein function from 3D structure. |
Nucleic Acids Res. 33(Web Server issue):W89-93 |
Annotation |
|
|
|
| Leontovich, Nikolaev et al |
Adaptive algorithm of automated annotation |
Bioinformatics 2002, 18 (6), 838-846. |
Annotation |
|
|
|
| Levy ED, Ouzounis CA, Gilks WR, Audit B. |
Probabilistic annotation of protein sequences based on functional classifications. |
BMC Bioinformatics. 2005 Dec 14;6:302. |
Annotation |
Probabiliste |
|
Estimation des erreurs |
| Marchler-Bauer A, Anderson JB, Cherukuri PF, DeWeese-Scott C, Geer LY, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Marchler GH, Mullokandov M, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Yamashita RA, Yin JJ, Zhang D, Bryant SH. |
CDD: a Conserved Domain Database for protein classification. |
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D192-6. |
Annotation |
|
|
|
| Marcotte EM |
Computational genetics: finding protein function by non homology methods |
Curr Opin Struct Biol 2000, 18:609-13 |
Annotation |
|
|
|
| Martin DM, Berriman M, Barton GJ. |
GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. |
BMC Bioinformatics. 2004 Nov 18;5:178. |
Annotation |
Non. Prédiction basée sur term-specific probability (P-scores) measures + seuil de cutoff (défini selon espèce) |
|
|
| Myers CL, Barrett DR, Hibbs MA, Huttenhower C, Troyanskaya OG. |
Finding function: evaluation methods for functional genomic data. |
BMC Genomics. 2006 Jul 25;7:187. |
Annotation |
|
|
|
| Nikolski M, Sherman DJ. |
Family relationships: should consensus reign?--consensus clustering for protein families. |
Bioinformatics. 2007 Jan 15;23(2):e71-6. |
Annotation |
|
|
|
| Sakata K, Nagamura Y, Numa H, Antonio BA, Nagasaki H, Idonuma A, Watanabe W, Shimizu Y, Horiuchi I, Matsumoto T, Sasaki T, Higo K. |
RiceGAAS: An Automated System for Rice Genome |
Genome Informatics 2001, 12, 496-497. |
Annotation |
Prédiction HMM |
O.sativa |
|
| Ouzounis CA, Karp PD. |
The past, present and future of genome-wide re-annotation. |
Genome Biol. 2002;3(2):COMMENT2001. Epub 2002 Jan 31. Review. |
Annotation |
|
|
|
| Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Ruckert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. |
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. |
Nucleic Acids Res. 2005 Oct 7;33(17):5691-702. Print 2005. |
Annotation |
Non |
Procaryotes, « subsystems simples » (enzyme d'une voie métabolique, élément d'un complexe, ...) ie. Rôle simple / fonction unique |
Système de récolte des expertises des experts d'un sous-système sur plusieurs génomes |
| Pal D, Eisenberg D. |
Inference of protein function from protein structure. |
Structure. 2005 Jan;13(1):121-30. |
Annotation |
|
|
ProKnow |
| Parra G, Bradnam K, Korf I. |
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. |
Bioinformatics. 2007 May 1;23(9):1061-7. Epub 2007 Mar 1. |
Annotation |
Non |
Eucaryotes |
Annotation structurale |
| Pazos F, Sternberg MJ. |
Automated prediction of protein function and detection of functional sites from structures |
PNAS, 2004, 101 (41), 14754-14759 |
Annotation |
|
|
PHUNCTIONER |
| Rigoutsos I, Huynh T, Floratos A, Parida L, Platt D. |
Dictionary-driven protein annotation. |
Nucleic Acids Res. 2002 Sep 1;30(17):3901-16. |
Général |
Statistique des séquences |
Méthode lente |
ré-annotation intégrée (70 génomes) ; dictionary = ensemble des paramètres mesurables pour une séquence protéique (analyse linguistique des seq. associée à la position) |
| Riley MC, Clare A, King RD. |
Locational distribution of gene functional classes in Arabidopsis thaliana. |
BMC Bioinformatics. 2007 Mar 30;8:112. |
Annotation Structure |
Non |
A.thaliana |
|
| Rivals I, Personnaz L, Taing L, Potier MC. |
Enrichment or depletion of a GO category within a class of genes: which test? |
Bioinformatics. 2007 Feb 15;23(4):401-7. Epub 2006 Dec 20. |
Annotation |
|
|
|
| Rudd S, Mewes HW, Mayer KF. |
Sputnik: a database platform for comparative plant genomics. |
Nucleic Acids Res. 2003 Jan 1;31(1):128-32. |
Annotation |
|
|
|
| Sasson O, Kaplan N, Linial M. |
Functional annotation prediction:All for one and one for all |
Protein Science 2006, 15:1557-1562. |
Annotation |
|
|
|
| Schlitt T, Brazma A. |
Modelling in molecular biology: describing transcription regulatory networks at different scales. |
Philos Trans R Soc Lond B Biol Sci. 2006 Mar 29;361(1467):483-94. Review. |
Général |
Infèrent la fonction à partir des topologies des réseaux de régulation |
|
|
| Schlitt T, Palin K, Rung J, Dietmann S, Lappe M, Ukkonen E, Brazma A. |
From gene networks to gene function.
|
Genome Res. 2003 Dec;13(12):2568-76. |
Annotation |
|
|
|
| Prlić A, Domingues FS, Lackner P, Sippl MJ. |
WILMA-automated annotation of protein sequences |
Bioinformatics. 2004 Jan 1;20(1):127-8. |
Annotation |
|
|
Système de requêtes utilisant GO qui permet d'identifier des séquences à différents niveaux (lien GO--> InterPro) |
| Teber ET, Crawford E, Bolton KB, Van Dyk D, Schofield PR, Kapoor V, Church WB. |
Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration. |
BMC Bioinformatics. 2006 Jan 23;7:33. |
Annotation |
|
Alignements transcrits/génomique, épissage alternatif |
Djinn Lite |
| Troyanskaya OG, Dolinski K, Owen AB, Altman RB, Botstein D. |
A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). |
Proc Natl Acad Sci U S A. 2003 Jul 8;100(14):8348-53. Epub 2003 Jun 25. |
Annotation |
|
|
MAGIC |
| Vallenet D, Labarre L, Rouy Z, Barbe V, Bocs S, Cruveiller S, Lajus A, Pascal G, Scarpelli C, Medigue C. |
MaGe: a microbial genome annotation system supported by synteny results. |
Nucleic Acids Res. 2006 Jan 10;34(1):53-65. Print 2006. |
Annotation |
|
|
MaGe |
| Vinayagam A, del Val C, Schubert F, Eils R, Glatting KH, Suhai S, Konig R. |
GOPET: a tool for automated predictions of Gene Ontology terms. |
BMC Bioinformatics. 2006 Mar 20;7:161. |
Annotation |
SVM (data=prot. 16 organismes + Swissprot ; appr. cDNA des 16 génomes) ; recall at 80% precision 65% |
Eucaryotes |
GOPET : Gene Ontology term Prediction and Evaluation |
| Weinel C, Ermolaeva MD, Ouzounis C. |
PseuRECA: genome annotation and gene context analysis for Pseudomonas aeruginosa PAO1. |
Bioinformatics. 2003 Aug 12;19(12):1457-60. |
Annotation |
|
|
|
| Wieser D, Kretschmann E, Apweiler R. |
Filtering erroneous protein annotation |
Bioinformatics 2004, 20 Suppl I:I342-I347. |
Annotation |
|
|
|
| Wieser, Apweiler et al |
Improving the Automated Annotation Process on Protein Data from TrEMBL by introducing Exclusion rules |
EBI Technical report |
Annotation |
|
|
|
| Wu CH, Huang H, Yeh LS, Barker WC. |
Protein family classification and functional annotation |
Comput Biol Chem. 2003 Feb;27(1):37-47. |
Annotation |
|
|
|
| Zhou CL, Lann MW, Smith JR, Zemla AT, Dyer MD, Kuczmarski TA, Vitalis EA, Slezak TR. |
MannDB - a microbial database of automated protein sequence analyses and evidence integration for protein characterization. |
BMC Bioinformatics. 2006 Oct 17;7:459. |
Annotation |
|
|
MannDB |