Solving the problem: Genome annotation standards before the data deluge

Standards in Genomic Sciences

Volumn 5, Issue 1, 2011, Pages 168-193

  Klimke, William ^a   O'Donovan, Claire ^b   White, Owen ^c   Brister, J Rodney ^a   Clark, Karen ^a   Fedorov, Boris ^a   Mizrachi, Ilene ^a   Pruitt, Kim D ^a   Tatusova, Tatiana ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROKARYOTA;

EID: 80054853710     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.2084864     Document Type: Article

References (82)

1. Bork P, Ouzounis C, Sander C, Scharf M, Schneider R, Sonnhammer E. Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III. Protein Sci 1992; 1:1677-1690. PubMed doi:10.1002/pro.5560011216
2. Bork P, Ouzounis C, Sander C, Scharf M, Schneider R, Sonnhammer E. What's in a genome? Nature 1992; 358:287. PubMed doi:10.1038/358287a0
3. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995; 269:496-512. PubMed doi:10.1126/science.7542800 4.
4. Madupu R, Brinkac LM, Harrow J, Wilming LG, Bohme U, Lamesch P, Hannick LI. Meeting re-port: a workshop on Best Practices in Genome Annotation. Database (Oxford) 2010;2010:baq001.
5. White O, Kyrpides N. Meeting Report: Towards a Critical Assessment of Functional Annotation Ex-periment (CAFAE) for bacterial genome annota-tion. Stand Genomic Sci 2010; 3:240-242. PubMed doi:10.4056/sigs.1323436
6. Ouzounis CA, Karp PD. The past, present and future of genome-wide re-annotation. Genome Biol 2002;3(2):COMMENT2001.
7. Ouzounis C, Bork P, Casari G, Sander C. New protein functions in yeast chromosome VIII. Pro-tein Sci 1995; 4:2424-2428. PubMed doi:10.1002/pro.5560041121
8. Kyrpides NC. Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream. Nat Biotechnol 2009; 27:627-632. PubMed doi:10.1038/nbt.1552
9. Klimke W, Tatusova T. Microbial Genomes at NCBI. Apweiler NMaR, editor. New York: Nova Science Publishers, Inc.; 2006.
10. Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res; 38(Database issue):D346-54.
11. Fraser CM, Eisen JA, Nelson KE, Paulsen IT, Salz-berg SL. The value of complete microbial genome sequencing (you get what you pay for). J Bacteriol 2002;184(23):6403-5; discusion 6405.
12. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010; 11:31-46. PubMed doi:10.1038/nrg2626
13. Schnoes AM, Brown SD, Dodevski I, Babbitt PC. Annotation error in public databases: misannotation of molecular function in enzyme super families. PLOS Comput Biol 2009; 5:e1000605. PubMed doi:10.1371/journal.pcbi.1000605
14. Dall'Olio GM, Bertranpetit J, Laayouni H. The annotation and the usage of scientific databases could be improved with public issue tracker soft-ware. Database (Oxford) 2010; 2010:baq035. PubMed doi:10.1093/database/baq035
15. Ussery DW, Hallin PF. Genome Update: annotation quality in sequenced microbial genomes. Mi-crobiology 2004; 150:2015-2017. PubMed doi:10.1099/mic.0.27338-0
16. Andorf C, Dobbs D, Honavar V. Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach. BMC Bioinformatics 2007; 8:284. PubMed doi:10.1186/1471-2105-8-284
17. Galperin MY, Nikolskaya AN, Koonin EV. Novel domains of the prokaryotic two-component signal transduction systems. FEMS Microbiol Lett 2001; 203:11-21. PubMed doi:10.1111/j.1574-6968.2001.tb10814.x
18. Pei J, Grishin NV. GGDEF domain is homologous to adenylyl cyclase. Proteins 2001; 42:210-216. PubMed doi:10.1002/1097-0134(20010201)42:2<210::AID-PROT80>3.0.CO;2-8
19. Römling U, Gomelsky M, Galperin MY. C-di-GMP: the dawning of a novel bacterial signalling system. Mol Microbiol 2005; 57:629-639. PubMed doi:10.1111/j.1365-2958.2005.04697.x
20. Rentzsch R, Orengo CA. Protein function prediction--the power of multiplicity. Trends Biotechnol 2009; 27:210-219. PubMed doi:10.1016/j.tibtech.2009.01.002
21. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955-964. PubMed doi:10.1093/nar/25.5.955
22. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucle-ic Acids Res 2007; 35:3100-3108. PubMed doi:10.1093/nar/gkm160
23. Glasner JD, Rusch M, Liss P, Plunkett G, Cabot EL, Darling A, Anderson BD, Infield-Harm P, Gil-son MC, Perna NT. ASAP: a resource for annotat-ing, curating, comparing, and disseminating ge-nomic data. Nucleic Acids Res 2006; 34(Database issue):D41-D45. PubMed doi:10.1093/nar/gkj164
24. Greene JM, Collins F, Lefkowitz EJ, Roos D, Scheuermann RH, Sobral B, Stevens R, White O, Di Francesco V. National Institute of Allergy and Infectious Diseases bioinformatics resource cen-ters: new assets for pathogen informatics. Infect Immun 2007; 75:3212-3219. PubMed doi:10.1128/IAI.00105-07
25. Pruitt KD, Tatusova T, Klimke W, Maglott DR. NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res 2009; 37(Database issue):D32-D36. PubMed doi:10.1093/nar/gkn721
26. Klimke W, Agarwala R, Badretdin A, Chetvernin S, Ciufo S, Fedorov B, Kiryutin B, O'Neill K, Resch W, Resenchuk S, et al. The National Center for Biotechnology Information's Protein Clusters Database. Nucleic Acids Res 2009; 37(Database issue):D216-D223. PubMed doi:10.1093/nar/gkn734
27. The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res 2009; 37(Database is-sue):D169-D174. PubMed doi:10.1093/nar/gkn664
28. Kersey P, Bower L, Morris L, Horne A, Petryszak R, Kanz C, Kanapin A, Das U, Michoud K, Phan I, et al. Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. Nucleic Acids Res 2004; 33(Database is-sue):D297-D302. PubMed doi:10.1093/nar/gki039
29. Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzge-rald S and others. Ensembl 2011. Nucleic Acids Res;39(Database issue):D800-6.
30. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 2001; 29:365-371. PubMed doi:10.1038/ng1201-365
31. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, An-giuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547. PubMed doi:10.1038/nbt1360
32. Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, et al. Promoting coherent minimum re-porting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol 2008; 26:889-896. PubMed doi:10.1038/nbt.1411
33. Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, et al. Towards BioDBcore: a community-defined information specification for biologi-cal databases. Nucleic Acids Res 2011; 39(Database issue):D7-D10. PubMed doi:10.1093/nar/gkq1173
34. Quackenbush J. Data reporting standards: making the things we use better. Genome Med 2009; 1:111. PubMed doi:10.1186/gm111
35. Kaminuma E, Mashima J, Kodama Y, Gojobori T, Ogasawara O, Okubo K, Takagi T, Nakamura Y. DDBJ launches a new archive database with ana-lytical tools for next-generation sequence data. Nucleic Acids Res 2010; 38(Database issue):D33-D38. PubMed doi:10.1093/nar/gkp847
36. Leinonen R, Akhtar R, Birney E, Bower L, Cerde-no-Tarraga A, Cheng Y, Cleland I, Faruque N, Goodgame N, Gibson R, et al. The European Nucleotide Archive. Nucleic Acids Res 2011; 39(Database issue):D28-D31. PubMed doi:10.1093/nar/gkq967
37. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kane-hisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007;35(Web Server issue):W182-5.
38. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, et al. The RAST Server: rapid annota-tions using subsystems technology. BMC Genom-ics 2008; 9:75. PubMed doi:10.1186/1471-2164-9-75
39. JGI website. http://www.jgi.doe.gov
40. Goll J, Montgomery R, Brinkac LM, Schobel S, Harkins DM, Sebastian Y, Shrivastava S, Durkin S, Sutton G. The Protein Naming Utility: a rules da-tabase for protein nomenclature. Nucleic Acids Res 2010; 38(Database issue):D336-D339. PubMed doi:10.1093/nar/gkp958
41. Antonov I, Borodovsky M. Genetack: frameshift identification in protein-coding sequences by the Viterbi algorithm. J Bioinform Comput Biol 2010; 8:535-551. PubMed doi:10.1142/S0219720010004847
42. Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Federhen S, et al. Database re-sources of the National Center for Biotechnology Information. Nucleic Acids Res 2011; 39(Database issue):D38-D51. PubMed doi:10.1093/nar/gkq1172
43. Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Kese-ler IM, Kosuge T, et al. Escherichia coli K-12: a cooperatively developed annotation snapshot--2005. Nucleic Acids Res 2006; 34:1-9. PubMed doi:10.1093/nar/gkj405
44. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 2006; 34(Database issue):D32-D36. PubMed doi:10.1093/nar/gkj014
45. Roberts AP, Chandler M, Courvalin P, Guedon G, Mullany P, Pembroke T, Rood JI, Smith CJ, Sum-mers AO, Tsuda M, et al. Revised nomenclature for transposable genetic elements. Plasmid 2008; 60:167-173. PubMed doi:10.1016/j.plasmid.2008.08.001
46. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, et al. The COG database: an updated version includes euka-ryotes. BMC Bioinformatics 2003; 4:41. PubMed doi:10.1186/1471-2105-4-41
47. Lima T, Auchincloss AH, Coudert E, Keller G, Michoud K, Rivoire C, Bulliard V, de Castro E, Lachaize C, Baratin D, et al. HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. Nucleic Acids Res 2009; 37(Database issue):D471-D478. PubMed doi:10.1093/nar/gkn661
48. Aoki-Kinoshita KF, Kanehisa M. Gene annotation and pathway mapping in KEGG. Methods Mol Biol 2007; 396:71-91. PubMed doi:10.1007/978-1-59745-515-2_6
49. Selengut JD, Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, Nelson WC, Richter AR, White O. TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biolog-ical process in prokaryotic genomes. Nucleic Ac-ids Res 2007; 35(Database issue):D260-D264. PubMed doi:10.1093/nar/gkl1043
50. Leplae R, Lima-Mendez G, Toussaint A. ACLAME: a CLAssification of Mobile genetic Elements, up-date 2010. Nucleic Acids Res 2010; 38(Database issue):D57-D61. PubMed doi:10.1093/nar/gkp938
51. Genome Annotation Workshop NCBI. http://www.ncbi.nlm.nih.gov/genomes/AnnotationWorkshop.html
52. Pruitt KD, Harrow J, Harte RA, Wallin C, Diek-hans M, Maglott DR, Searle S, Farrell CM, Lovel JE, Ruef BJ, et al. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res 2009; 19:1316-1323. PubMed doi:10.1101/gr.080531.108
53. Blattner FR, Plunkett G, III, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, et al. The complete genome sequence of Escherichia coli K-12. Science 1997; 277:1453-1462. PubMed doi:10.1126/science.277.5331.1453
54. Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, Muniz-Rascado L, Bonavides-Martinez C, Paley S, Krummenacker M, Altman T, et al. EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res 2011; 39(Database issue):D583-D590. PubMed doi:10.1093/nar/gkq1143
55. Rudd KE. EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 2000; 28:60-64. PubMed doi:10.1093/nar/28.1.60
56. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res 2011; 39(Database issue):D32-D37. PubMed doi:10.1093/nar/gkq1079
57. BioProject. http://www.ncbi.nlm.nih.gov/genomeprj
58. Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity G, Kodira CD, Kyrpides N, Ma-dupu R, Markowitz V, et al. Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. OMICS 2008; 12:137-141. PubMed doi:10.1089/omi.2008.0017
59. Winsor GL, Van Rossum T, Lo R, Khaira B, Whi-teside MD, Hancock RE, Brinkman FS. Pseudo-monas Genome Database: facilitating user-friendly, comprehensive comparisons of microbi-al genomes. Nucleic Acids Res 2009; 37(Database issue):D483-D488. PubMed doi:10.1093/nar/gkn861
60. The Gene Ontology in. extensions and refinements. Nucleic Acids Res 2010; 38(Database issue):D331-D335. PubMed
61. Gil R, Silva FJ, Pereto J, Moya A. Determination of the core of a minimal bacterial gene set. Micro-biol Mol Biol Rev 2004; 68:518-537. PubMed doi:10.1128/MMBR.68.3.518-537.2004
62. Harris JK, Kelley ST, Spiegelman GB, Pace NR. The genetic core of the universal ancestor. Ge-nome Res 2003; 13:407-412. PubMed doi:10.1101/gr.652803
63. Lipman DJ, Souvorov A, Koonin EV, Panchenko AR, Tatusova TA. The relationship of protein con-servation and sequence length. BMC Evol Biol 2002; 2:20. PubMed doi:10.1186/1471-2148-2-20
64. Giovannoni SJ, Tripp HJ, Givan S, Podar M, Ver-gin KL, Baptista D, Bibbs L, Eads J, Richardson TH, Noordewier M, et al. Genome streamlining in a cosmopolitan oceanic bacterium. Science 2005; 309:1242-1245. PubMed doi:10.1126/science.1114057
65. Nakabachi A, Yamashita A, Toh H, Ishikawa H, Dunbar HE, Moran NA, Hattori M. The 160-kilobase genome of the bacterial endosymbiont Carsonella. Science 2006; 314:267. PubMed doi:10.1126/science.1134196
66. McCutcheon JP, McDonald BR, Moran NA. Origin of an alternative genetic code in the extremely small and GC-rich genome of a bacterial symbiont. PLoS Genet 2009; 5:e1000565. PubMed doi:10.1371/journal.pgen.1000565
67. Dufresne A, Garczarek L, Partensky F. Accele-rated evolution associated with genome reduction in a free-living prokaryote. Genome Biol 2005; 6:R14. PubMed doi:10.1186/gb-2005-6-2-r14
68. Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, Arellano A, Coleman M, Hauser L, Hess WR, et al. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 2003; 424:1042-1047. PubMed doi:10.1038/nature01947
69. Willenbrock H, Binnewies TT, Hallin PF, Ussery DW. Genome update: 2D clustering of bacterial genomes. Microbiology 2005; 151:333-336. PubMed doi:10.1099/mic.0.27811-0
70. Moran NA, McLaughlin HJ, Sorek R. The dynam-ics and time scale of ongoing genomic erosion in symbiotic bacteria. Science 2009; 323:379-382. PubMed doi:10.1126/science.1167140
71. Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H. Genome sequence of the endocellu-lar bacterial symbiont of aphids Buchnera sp. APS. Nature 2000; 407:81-86. PubMed doi:10.1038/35024074
72. Shen X, Wang Q, Xia L, Zhu X, Zhang Z, Liang Y, Cai H, Zhang E, Wei J, Chen C, et al. Complete genome sequences of Yersinia pestis from natural foci in China. J Bacteriol 2010; 192:3551-3552. PubMed doi:10.1128/JB.00340-10
73. Jeong H, Barbe V, Lee CH, Vallenet D, Yu DS, Choi SH, Couloux A, Lee SW, Yoon SH, Cattolico L, et al. Genome sequences of Escherichia coli B strains REL606 and BL21(DE3). J Mol Biol 2009; 394:644-652. PubMed doi:10.1016/j.jmb.2009.09.052
74. Karro JE, Yan Y, Zheng D, Zhang Z, Carriero N, Cayting P, Harrrison P, Gerstein M. Pseudo-gene.org: a comprehensive database and compar-ison platform for pseudogene annotation. Nucleic Acids Res 2007; 35(Database issue):D55-D60. PubMed doi:10.1093/nar/gkl851
75. Liu Y, Harrison PM, Kunin V, Gerstein M. Com-prehensive analysis of pseudogenes in proka-ryotes: widespread gene decay and failure of put-ative horizontally transferred genes. Genome Biol 2004; 5:R64. PubMed doi:10.1186/gb-2004-5-9-r64
76. Kuo CH, Ochman H. The extinction dynamics of bacterial pseudogenes. PLoS Genet 2010; 6. PubMed doi:10.1371/journal.pgen.1001050
77. Okuda S, Yamada T, Hamajima M, Itoh M, Ka-tayama T, Bork P, Goto S, Kanehisa M. KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res 2008;36(Web Server issue):W423-6.
78. Koonin EV, Wolf YI. Genomics of bacteria and archaea: the emerging dynamic view of the pro-karyotic world. Nucleic Acids Res 2008; 36:6688-6719. PubMed doi:10.1093/nar/gkn668
79. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial pan-genome. Proc Natl Acad Sci USA 2005; 102:13950-13955. PubMed doi:10.1073/pnas.0506758102
80. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, et al. InterPro: the integrative pro-tein signature database. Nucleic Acids Res 2009; 37(Database issue):D211-D215. PubMed doi:10.1093/nar/gkn785
81. Brister JR, Bao Y, Kuiken C, Lefkowitz EJ, Le Mer-cier P, Leplae R, Madupu R, Scheuermann RH, Schobel S, Seto D, et al. Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop. Viruses 2010; 2:2258-2268. doi:10.3390/v2102258
82. Roberts RJ, Chang YC, Hu Z, Rachlin JN, Anton BP, Pokrzywa RM, Choi HP, Faller LL, Guleria J, Housman G, et al. COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. Nucleic Acids Res 2011; 39(Database issue):D11-D14. PubMed doi:10.1093/nar/gkq1168