An extensible automated protein annotation tool: Standardizing input and output using validated XML

Bioinformatics

Volumn 22, Issue 3, 2006, Pages 291-296

  Deevi, S Vishnu S ^a   Martin, Andrew C R ^b  

^a UNIVERSITY OF READING   (United Kingdom)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATED PROTEIN ANNOTATION TOOL; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; COMPUTER PREDICTION; COMPUTER PROGRAM; INFORMATION PROCESSING; INTERNET; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN DOMAIN; SEQUENCE ANALYSIS; STANDARDIZATION; STRUCTURAL PROTEOMICS;

EID: 32144434540     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti808     Document Type: Article

References (36)

1. Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
3. Apweiler,R. et al. (2001) The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res., 29, 37-40.
4. Ashburner,M. et al. (2000) Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
5. Bairoch,A. and Apweiler,R. (2000) The Swiss-Prot protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res., 28, 45-48.
6. Blom,N. et al. (1999) Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J. Mol. Biol., 294, 1351-1362.
7. Boeckmann,B. et al. (2003) The Swiss-Prot Protein Knowledge base and its supplement TrEMBL in 2003. Nucleic Acids Res., 31. 365-370.
8. Cserzo,M. et al. (2004) TM or not TM: Transmembrane protein prediction with low false positive rate using DAS-TMfilter. Bioinformatics, 20, 136-137.
9. Dowell,R.D. et al. (2001) The distributed annotation system. BMC Bioinformatics, 2, 7.
10. Durinck,S. et al. (2005) BioMart and Bioconductor: A powerful link between biological databases and microarray data analysis. Bioinformatics, 21, 3439-3440.
11. Eckart,J.D. and Sobral,B.W. (2003) A life scientist's gateway to distributed data management and computing: The PathPort/ToolBus framework. OMICS, 7, 79-88.
12. Emanuelsson,O. et al. (2000) Predicting subcellular localisation of proteins based on their N-terminal amino acid sequence. J. Mol. Biol., 300, 1005-1016.
13. Frishman,D. et al. (2001) Functional and structural genomics using PEDANT. Bioinformatics, 17, 44-57.
14. Gattiker,A. et al. (2002) ScanProsite: A reference implementation of a PROSITE scanning tool. Appl. Bioinformatics, 1. 107-108.
15. Hoon,S. et al. (2003) Biopipe: A flexible framework for protocol-based bioinformatics analysis. Genome Res., 13, 1904-1915.
16. Hubbard,T. et al. (2002) The Ensembl genome database project. Nucleic Acids Res., 30, 38-41.
17. Hulo,N. et al. (2004) Recent improvements to the PROSITE database. Nucleic Acids Res., 32, D134-D137.
18. Julenius,K. et al. (2004) Prediction, conservation analysis and structural characterisation of mammalian mucin-type O-glycosylation sites. Glycobiology 15, 153-164.
19. Krogh,A. et al. (2001) Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol., 305, 567-580.
20. Laskowski,R.A. (2001) PDBsum: Summaries and analyses of PDB structures. Nucleic Acids Res., 29, 221-222.
21. McGuffin,L.J. et al. (2000) The PSIPRED protein structure prediction server. Bioinformatics, 16, 404-405.
22. Milburn,D. et al. (1998) Sequences annotated by structure: A tool to facilitate the use of structural information in sequence analysis. Protein Eng., 11, 855-859.
23. Nair,R. and Rost,B. (2004) LOCnet and LOCtarget: Sub-cellular localisation for structural genomics targets. Nucleic Acids Res., 32, W517-W521.
24. Nayal,M. et al. (1999) GRASS: A server for the graphical representation and analysis of structures. Protein Sci., 8, 676-679.
25. Neshich,G. et al. (2003) STING Millennium: A web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence. Nucleic Acids Res., 31, 3386-3392.
26. Oinn,T.M. (2003) Talisman - rapid application development for the grid. Bioinformatics, 19 (Suppl. 1), i212-i214.
27. Oinn,T. et al. (2004) Taverna: A tool for the composition and enactment of bioinformatics workflows. Bioinformatics, 20, 3045-3054.
28. Pruess,M. et al. (2005) The Integr8 project - a resource for genomic and proteomic data. In Silico Biol., 5, 179-I85.
29. Rost,B. (1996) PHD: Predicting one-dimensional protein structure by profile-based neural networks. Methods Enzymol., 266, 525-539.
30. Schultz,J. et al. (1998) SMART, a simple modular architecture research tool: Identification of signaling domains. Proc. Natl Acad Sci. USA, 95, 5857-5864.
31. Scordis,P. et al. (1999) FingerPRINTScan: Intelligent searching of the PRINTS motif database. Bioinformatics, 15, 799-806.
32. Senger,M. et al. (2003) SoapLab - a unified sesame door to analysis tools. In Proceedings of the UK e-Science All Hands Meeting 2003, September 2-4, Nottingham UK, pp. 509-513.
33. Siepel,A. et al. (2001) ISYS: A decentralised, component-based approach to the integration of heterogeneous bioinformatics resources. Bioinformatics, 17, 83-94.
34. Small,J. et al. (2004) Predotar: A tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics, 4, 1581-1590.
35. Zdobnov,E.M. and Apweiler,R. (2001) InterProScan - an integration platform for the signature-recognition methods in interPro. Bioinformatics, 17, 847-848.
36. Zuegge,J. et al. (2001) Deciphering apicoplast targeting signals feature extraction from nuclear-encoded precursors of plasmodium falciparum apicoplast proteins. Gene, 280, 19-26.