AutoFACT: An automatic functional annotation and classification tool

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Koski, Liisa B ^a   Gray, Michael W ^b   Lang, B Franz ^a   Burger, Gertraud ^a  

^a Universite de Montreal   (Canada)

^b DALHOUSIE UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ANNOTATION METHODS; AUTOMATIC FUNCTIONAL ANNOTATION; CLASSIFICATION TOOL; FUNCTIONAL ANNOTATION; FUNCTIONAL CLASS; METABOLIC PATHWAYS; PROTEIN SEQUENCE DATA; SIMILARITY SEARCH;

BIOINFORMATICS;

TOOLS;

ACANTHAMOEBA CASTELLANII; AMINO ACID SEQUENCE; ANALYTICAL ERROR; ARTICLE; AUTOMATION; BIOINFORMATICS; COMPUTER PROGRAM; CONTROLLED STUDY; GENE LOCUS; GENE SEQUENCE; GENETIC DATABASE; GENOMICS; HUMAN; HYPERMEDIA; METABOLISM; METHODOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMODIUM FALCIPARUM; RICKETTSIA PROWAZEKII; SACCHAROMYCES CEREVISIAE; ANIMAL; BIOLOGY; CLASSIFICATION; CONTIG MAPPING; DEVICES; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENETICS; INFORMATION SYSTEM; INTERNET; PHYLOGENY; PROCEDURES; SEQUENCE ALIGNMENT; VALIDATION STUDY;

COMPLEMENTARY DNA;

ACANTHAMOEBA CASTELLANII; ANIMALS; COMPUTATIONAL BIOLOGY; CONTIG MAPPING; DATABASES, GENETIC; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; HUMANS; INFORMATION MANAGEMENT; INTERNET; PHYLOGENY; PLASMODIUM FALCIPARUM; RICKETTSIA PROWAZEKII; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE; SOFTWARE VALIDATION;

EID: 25444458848     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-151     Document Type: Article

References (33)

1. LG Almeida, R Paixao, RC Souza, GC Da Costa, FJ Barrientos, MT Dos Santos, DF De Almeida, AT Vasconcelos: A system for automated bacterial (genome) integrated annotation - SABIA. Bioinformatics 2004.
2. P Ayoubi, X Jin, S Leite, X Liu, J Martajaja, A Abduraham, Q Wan, W Yan, E Misawa, RA Prade: PipeOnline 2.0: automated EST processing and functional data sorting. Nucleic Acids Res 2002, 30:4761-9.
3. JM Buerstedde, F Prill: FOUNTAIN: a JAVA open-source package to assist large sequencing projects. BMC Bioinformatics 2001, 2:6.
4. SK Wyman, RK Jansen, JL Boore: Automatic annotation of organellar genomes with DOGMA. Bioinformatics 2004, 20:3252-5.
5. MA Andrade, NP Brown, C Leroy, S Hoersch, A de Daruvar, C Reich, A Franchini, J Tamames, A Valencia, C Ouzounis, C Sander: Automated genome sequence analysis and annotation. Bioinformatics 1999, 15:391-412.
6. F Abascal, A Valencia: Automatic annotation of protein function based on family identification. Proteins 2003, 53:683-92.
7. E Birney, M Clamp, R Durbin: GeneWise and Genomewise. Genome Res 2004, 14:988-95.
8. V Curwen, E Eyras, TD Andrews, L Clarke, E Mongin, SM Searle, M Clamp: The Ensembl automatic gene annotation system. Genome Res 2004, 14:942-50.
9. S Moller, U Leser, W Fleischmann, R Apweiler: EDITtoTrEMBL: a distributed approach to high-quality automated protein sequence annotation. Bioinformatics 1999, 15:219-27.
10. bioperl.org.www.bioperl.org.
11. NCBI BLAST.www.ncbi.nih.gov/BLAST.
12. NCBI Education BLAST info Glossary. www.ncib.nlm.nih.gov/Education/BLASTinfo/glossary2.html.
13. SF Altschul, W Gish, W Miller, EW Myers, DJ Lipman: Basic local alignment search tool. J Mol Biol 1990, 215:403-10.
14. AJ Barrett: Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB). Enzyme Nomenclature. Recommendations 1992. Supplement 4: corrections and additions (1997). Eur J Biochem 1997, 250:1-6.
15. E Gasteiger, A Gattiker, C Hoogland, I Ivanyi, RD Appel, A Bairoch: ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 2003, 31:3784-8.
16. E Camon, M Magrane, D Barrell, V Lee, E Dimmer, J Maslen, D Binns, N Harte, R Lopez, R Apweiler: The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res 2004, 32 Database issue:D262-6.
17. GFF: An exchange format for Feature Description. www.sanger.ac.uk/Software/GFF.
18. D Frishman, K Albermann, J Hani, K Heumann, A Metanomski, A Zollner, HW Mewes: Functional and structural genomics using PEDANT. Bioinformatics 2001, 17:44-57.
19. D Frishman, M Mokrejs, D Kosykh, G Kastenmuller, G Kolesov, I Zubrzycki, C Gruber, B Geier, A Kaps, K Albermann, A Volz, C Wagner, M Fellenberg, K Heumann, HW Mewes: The PEDANT genome database. Nucleic Acids Res 2003, 31:207-11.
20. MJ Gardner, N Hall, E Fung, O White, M Berriman, RW Hyman, JM Carlton, A Pain, KE Nelson, S Bowman, IT Paulsen, K James, JA Eisen, K Rutherford, SL Salzberg, A Craig, S Kyes, MS Chan, V Nene, SJ Shallom, B Suh, J Peterson, S Angiuoli, M Pertea, J Allen, J Selengut, D Haft, MW Mather, AB Vaidya, DM Martin, AH Fairlamb, MJ Fraunholz, DS Roos, SA Ralph, GI McFadden, LM Cummings, GM Subramanian, C Mungall, JC Venter, DJ Carucci, SL Hoffman, C Newbold, RW Davis, CM Fraser, B Barrell: Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 2002, 419:498-511.
21. SG Andersson, A Zomorodipour, JO Andersson, T Sicheritz-Ponten, UC Alsmark, RM Podowski, AK Naslund, AS Eriksson, HH Winkler, CG Kurland: The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 1998, 396:133-40.
22. GeneQuiz; Rickettsia prowazekii. http://jura.ebi.ac.uk:8765/extgenequiz/genomes/rp0006.
23. PEPdb Pub; The Protist EST Database. http://amoebidia.bcm.umontreal.ca/public/pepdb/agrm.php.
24. BD Kurosky A, Lee TH, Touchstone B, Hay RE, Arnott MS, Bowman BH, Fitch WM.: Covalent structure of human haptoglobin: a serine protease homolog. Proc Natl Acad Sci U S A 1980, 77:3388-92.
25. J Wuyts, G Perriere, Y Van De Peer: The European ribosomal RNA database. Nucleic Acids Res 2004, 32:D101-3.
26. R Apweiler, A Bairoch, CH Wu, WC Barker, B Boeckmann, S Ferro, E Gasteiger, H Huang, R Lopez, M Magrane, MJ Martin, DA Natale, C O'Donovan, N Redaschi, LS Yeh: UniProt: the Universal Protein knowledgebase. Nucleic Acids Res 2004, 32 Database issue:D115-9.
27. RL Tatusov, ND Fedorova, JD Jackson, AR Jacobs, B Kiryutin, EV Koonin, DM Krylov, R Mazumder, SL Mekhedov, AN Nikolskaya, BS Rao, S Smirnov, AV Sverdlov, S Vasudevan, YI Wolf, JJ Yin, DA Natale: The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003, 4:41.
28. RL Tatusov, EV Koonin, DJ Lipman: A genomic perspective on protein families. Science 1997, 278:631-7.
29. M Kanehisa: A database for post-genome analysis. Trends Genet 1997, 13:375-6.
30. M Kanehisa, S Goto: KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28:27-30.
31. A Bateman, L Coin, R Durbin, RD Finn, V Hollich, S Griffiths-Jones, A Khanna, M Marshall, S Moxon, EL Sonnhammer, DJ Studholme, C Yeats, SR Eddy: The Pfam protein families database. Nucleic Acids Res 2004, 32 Database issue:D138-41.
32. J Schultz, F Milpetz, P Bork, CP Ponting: SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci U S A 1998, 95:5857-64.
33. National Center for Biotechnology Information. [http://www.ncbi.nlm.nih.gov].