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Resources for functional annotation

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Modern Genome Annotation

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Abstract

The continued success of genome sequencing projects has led to an explosion in the availability of sequence data. The Genomes On Line Database (GOLD) currently lists more than 2000 ongoing and completed genome projects, and this number is continuously increasing (Liolios et al. 2008). In order for this sequence information to be useful in the formulation and testing of biological hypotheses, these genome sequences must be adequately annotated.

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References

  • Andreeva A, Howorth D, Brenner SE, Hubbard TJ, Chothia C, Murzin AG (2004) SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res 32: D226–D229

    Article  PubMed  CAS  Google Scholar 

  • Attwood TK, Bradley P, Flower DR, Gaulton A, Maudling N, Mitchell AL, Moulton G, Nordle A, Paine K, Taylor P, Uddin A, Zygouri C (2003) PRINTS and its automatic supplement, prePRINTS. Nucleic Acids Res 31: 400–402

    Article  PubMed  CAS  Google Scholar 

  • Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL (2003) GenBank. Nucleic Acids Res 31: 23–27

    Article  PubMed  CAS  Google Scholar 

  • Berman H, Henrick K, Nakamura H, Markley JL (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res 35: D301–D303

    Article  PubMed  CAS  Google Scholar 

  • Bieri T, Blasiar D, Ozersky P, Antoshechkin I, Bastiani C, Canaran P, Chan J, Chen N, Chen WJ, Davis P, Fiedler TJ, Girard L, Han M, Harris TW, Kishore R, Lee R, McKay S, Muller HM, Nakamura C, Petcherski A, Rangarajan A, Rogers A, Schindelman G, Schwarz EM, Spooner W, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Durbin R, Stein LD, Sternberg PW, Spieth J (2007) WormBase: new content and better access. Nucleic Acids Res 35: D506–D510

    Article  PubMed  CAS  Google Scholar 

  • Bru C, Courcelle E, Carrere S, Beausse Y, Dalmar S, Kahn D (2005) The ProDom database of protein domain families: more emphasis on 3D. Nucleic Acids Res 33: D212–D215

    Article  PubMed  CAS  Google Scholar 

  • Camon E, Magrane M, Barrell D, Lee V, Dimmer E, Maslen J, Binns D, Harte N, Lopez R, Apweiler R (2004) The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with gene ontology. Nucleic Acids Res 32: D262–D266

    Article  PubMed  CAS  Google Scholar 

  • Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM (2004) Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res 32:D311–D314

    Article  PubMed  CAS  Google Scholar 

  • Cooper CA, Joshi HJ, Harrison MJ, Wilkins MR, Packer NH (2003) GlycoSuiteDB: a curated relational database of glycoprotein glycan structures and their biological sources. 2003 update. Nucleic Acids Res 31: 511–513

    Article  PubMed  CAS  Google Scholar 

  • Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM (2007) FlyBase: genomes by the dozen. Nucleic Acids Res 35: D486–D491

    Article  PubMed  CAS  Google Scholar 

  • Durbin R, Eddy S, Krogh A, Mitchison G (1998) Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge University Press, Cambridge, UK

    Google Scholar 

  • Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A (2006) Pfam: clans, web tools and services. Nucleic Acids Res 34: D247–D251

    Article  PubMed  CAS  Google Scholar 

  • Fleischmann W, Moller S, Gateau A, Apweiler R (1999) A novel method for automatic functional annotation of proteins. Bioinformatics 15: 228–233

    Article  PubMed  CAS  Google Scholar 

  • Garavelli JS (2004) The RESID Database of Protein Modifications as a resource and annotation tool. Proteomics 4: 1527–1533

    Article  PubMed  CAS  Google Scholar 

  • Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A (2003) ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 31: 3784–3788

    Article  PubMed  CAS  Google Scholar 

  • 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 (2003) Automated annotation of microbial proteomes in SWISS-PROT. Comput Biol Chem 27: 49–58

    Article  PubMed  CAS  Google Scholar 

  • Gene Ontology Consortium (2006) The Gene Ontology (GO) project in 2006. Nucleic Acids Res 34: D322–D326

    Article  CAS  Google Scholar 

  • Greene LH, Lewis TE, Addou S, Cuff A, Dallman T, Dibley M, Redfern O, Pearl F, Nambudiry R, Reid A, Sillitoe I, Yeats C, Thornton JM, Orengo CA (2007) The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res 35: D291–D297

    Article  PubMed  CAS  Google Scholar 

  • Gribskov M, Luthy R, Eisenberg D (1990) Profile analysis. Methods Enzymol 183: 146–159

    Article  PubMed  CAS  Google Scholar 

  • Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Fitzgerald S, Fernandez-Banet J, Graf S, Haider S, Hammond M, Herrero J, Holland R, Howe K, Johnson N, Kahari A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Melsopp C, Megy K, Meidl P, Ouverdin B, Parker A, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Severin J, Slater G, Smedley D, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wood M, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Flicek P, Kasprzyk A, Proctor G, Searle S, Smith J, Ureta-Vidal A, Birney E (2007) Ensembl 2007. Nucleic Acids Res 35: D610–D617

    Article  PubMed  CAS  Google Scholar 

  • Hulo N, Bairoch A, Bulliard V, Cerutti L, De Castro E, Langendijk-Genevaux PS, Pagni M, Sigrist CJ (2006) The PROSITE database. Nucleic Acids Res 34: D227–D230

    Article  PubMed  CAS  Google Scholar 

  • Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, Ahren D, Tsoka S, Darzentas N, Kunin V, Lopez-Bigas N (2005) Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res 33: 6083–6089

    Article  PubMed  CAS  Google Scholar 

  • Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, Dimmer E, Feuermann M, Friedrichsen A, Huntley R, Kohler C, Khadake J, Leroy C, Liban A, Lieftink C, Montecchi-Palazzi L, Orchard S, Risse J, Robbe K, Roechert B, Thorneycroft D, Zhang Y, Apweiler R, Hermjakob H (2007) IntAct — open source resource for molecular interaction data. Nucleic Acids Res 35: D561–D565

    Article  PubMed  CAS  Google Scholar 

  • Kersey P, Bower L, Morris L, Horne A, Petryszak R, Kanz C, Kanapin A, Das U, Michoud K, Phan I, Gattiker A, Kulikova T, Faruque N, Duggan K, McLaren P, Reimholz B, Duret L, Penel S, Reuter I, Apweiler R (2005) Integr8 and genome reviews: integrated views of complete genomes and proteomes. Nucleic Acids Res 33: D297–D302

    Article  PubMed  CAS  Google Scholar 

  • Kersey PJ, Duarte J, Williams A, Karavidopoulou Y, Birney E, Apweiler R (2004) The International Protein Index: an integrated database for proteomics experiments. Proteomics 4: 1985–1988

    Article  PubMed  CAS  Google Scholar 

  • Kopp J, Schwede T (2006) The SWISS-MODEL repository: new features and functionalities. Nucleic Acids Res 34: D315–D318

    Article  PubMed  CAS  Google Scholar 

  • Kretschmann E, Fleischmann W, Apweiler R (2001) Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT. Bioinformatics 17: 920–926

    Article  PubMed  CAS  Google Scholar 

  • Krogh A, Brown M, Mian IS, Sjolander K, Haussler D(1994) Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol 235: 1501–1531

    Article  PubMed  CAS  Google Scholar 

  • Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ, Thakkapallayil A, Sugnet CW, Stanke M, Smith KE, Siepel A, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pedersen JS, Hsu F, Hinrichs AS, Harte RA, Diekhans M, Clawson H, Bejerano G, Barber GP, Baertsch R, Haussler D, Kent WJ (2007) The UCSC genome browser database: update 2007. Nucleic Acids Res 35: D668–D673

    Article  PubMed  CAS  Google Scholar 

  • Leinonen R, Diez FG, Binns D, Fleischmann W, Lopez R, Apweiler R(2004) UniProt archive. Bioinformatics 20: 3236–3237

    Article  PubMed  CAS  Google Scholar 

  • Lenhard B, Hayes WS, Wasserman WW (2001) GeneLynx: a gene-centric portal to the human genome. Genome Res 11: 2151–2157

    Article  PubMed  CAS  Google Scholar 

  • Letunic I, Copley RR, Pils B, Pinkert S, Schultz J, Bork P (2006) SMART 5: domains in the context of genomes and networks. Nucleic Acids Res 34: D257–D260

    Article  PubMed  CAS  Google Scholar 

  • Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC (2008) The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 36: D475–D479

    Article  PubMed  CAS  Google Scholar 

  • McKusick VA (2007) Mendelian Inheritance in Man and its online version, OMIM. Am J Hum Genet 80: 588–604

    Article  PubMed  CAS  Google Scholar 

  • Mi H, Guo N, Kejariwal A, Thomas PD (2007) PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. Nucleic Acids Res 35: D247–D252

    Article  PubMed  CAS  Google Scholar 

  • Miyazaki S, Sugawara H, Gojobori T, Tateno Y (2003) DNA Data Bank of Japan (DDBJ) in XML. Nucleic Acids Res 31: 13–16

    Article  PubMed  CAS  Google Scholar 

  • Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, Fleischmann W, Gough J, Haft D, Hulo N, Hunter S, Kahn D, Kanapin A, Kejariwal A, Labarga A, Langendijk-Genevaux PS, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Nikolskaya AN, Orchard S, Orengo C, Petryszak R, Selengut JD, Sigrist CJ, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C (2007) New developments in the InterPro database. Nucleic Acids Res 35: D224–D228

    Article  PubMed  CAS  Google Scholar 

  • Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M (2006) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127: 635–648

    Article  PubMed  CAS  Google Scholar 

  • Pruitt KD, Tatusova T, Maglott DR (2007) NCBI reference sequences (RefSeq): a curated nonredundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35: D61–D65

    Article  PubMed  CAS  Google Scholar 

  • Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005) InterProScan: protein domains identifier. Nucleic Acids Res 33: W116–W120

    Article  PubMed  CAS  Google Scholar 

  • Safran M, Solomon I, Shmueli O, Lapidot M, Shen-Orr S, Adato A, Ben-Dor U, Esterman N, Rosen N, Peter I, Olender T, Chalifa-Caspi V, Lancet D (2002) GeneCards 2002: towards a complete, objectoriented, human gene compendium. Bioinformatics 18: 1542–1543

    Article  PubMed  CAS  Google Scholar 

  • Selengut JD, Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, Nelson WC, Richter AR, White O (2007) TIGRFAMs and genome properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res 35: D260–D264

    Article  PubMed  CAS  Google Scholar 

  • Stoesser G, Baker W, van den Broek A, Garcia-Pastor M, Kanz C, Kulikova T, Leinonen R, Lin Q, Lombard V, Lopez R, Mancuso R, Nardone F, Stoehr P, Tuli MA, Tzouvara K, Vaughan R (2003) The EMBL Nucleotide Sequence Database: major new developments. Nucleic Acids Res 31: 17–22

    Article  PubMed  CAS  Google Scholar 

  • Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH (2007) UniRef: comprehensive and nonredundant UniProt reference clusters. Bioinformatics 23: 1282–1288

    Article  PubMed  CAS  Google Scholar 

  • Tagari M, Tate J, Swaminathan GJ, Newman R, Naim A, Vranken W, Kapopoulou A, Hussain A, Fillon J, Henrick K, Velankar S (2006) E-MSD: improving data deposition and structure quality. Nucleic Acids Res 34: D287–D290

    Article  PubMed  CAS  Google Scholar 

  • Tamaki S, Arakawa K, Kono N, Tomita M (2007) Restauro-G: a rapid genome re-annotation system for comparative genomics. Genomics Proteomics Bioinformatics 5: 53–58

    Article  PubMed  CAS  Google Scholar 

  • The International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437: 1299–1320

    Article  CAS  Google Scholar 

  • UniProt Consortium (2007) The Universal Protein Resource (UniProt). Nucleic Acids Res 35: D193–D197

    Article  Google Scholar 

  • Vastrik I, D’Eustachio P, Schmidt E, Joshi-Tope G, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, Lewis S, Matthews L, Wu G, Birney E, Stein L (2007) Reactome: a knowledge base of biologic pathways and processes. Genome Biol 8: R39

    Article  PubMed  CAS  Google Scholar 

  • Wilson D, Madera M, Vogel C, Chothia C, Gough J (2007) The SUPERFAMILY database in 2007: families and functions. Nucleic Acids Res 35: D308–D313

    Article  PubMed  CAS  Google Scholar 

  • Wu CH, Nikolskaya A, Huang H, Yeh LS, Natale DA, Vinayaka CR, Hu ZZ, Mazumder R, Kumar S, Kourtesis P, Ledley RS, Suzek BE, Arminski L, Chen Y, Zhang J, Cardenas JL, Chung S, Castro-Alvear J, Dinkov G, Barker WC (2004) PIRSF: family classification system at the Protein Information Resource. Nucleic Acids Res 32: D112–D114

    Article  PubMed  CAS  Google Scholar 

  • Yeats C, Maibaum M, Marsden R, Dibley M, Lee D, Addou S, Orengo CA (2006) Gene3D: modelling protein structure, function and evolution. Nucleic Acids Res 34: D281–D284

    Article  PubMed  CAS  Google Scholar 

  • Yip YL, Scheib H, Diemand AV, Gattiker A, Famiglietti LM, Gasteiger E, Bairoch A (2004) The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants. Hum Mutat 23: 464–470

    Article  PubMed  CAS  Google Scholar 

  • Zdobnov EM, Apweiler R (2001) InterProScan — an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17: 847–848

    Article  PubMed  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. Swiss-Prot, Swiss-Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211, Geneva 4, Switzerland

    A. J. Bridge & A.-Lise Veuthey

  2. EMBL Outstation, European Bioinformatics Institute Hinxton, Cambridge, UK

    N. J. Mulder

Authors
  1. A. J. Bridge
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  2. A.-Lise Veuthey
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  3. N. J. Mulder
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Correspondence to A. J. Bridge .

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Editors and Affiliations

  1. Wissenschaftszentrum Weihenstephan, TU München, Freising, Germany

    Dmitrij Frishman

  2. Structural and Computational Programme, Spanish National Cancer Research Centre, Madrid, Spain

    Alfonso Valencia

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Bridge, A.J., Veuthey, AL., Mulder, N.J. (2008). Resources for functional annotation. In: Frishman, D., Valencia, A. (eds) Modern Genome Annotation. Springer, Vienna. https://doi.org/10.1007/978-3-211-75123-7_8

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