Methods for improving genome annotation

Knowledge-Based Bioinformatics: From Analysis to Interpretation

Volumn , Issue , 2010, Pages 209-232

  Mudge, Jonathan ^a   Harrow, Jennifer ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

Alignment free clustering method; Batch Learning SOM (BLSOM); Environmental microorganisms; Genome informatics; High performance supercomputer; Metagenome; Oligonucleotide frequency; Phylogenetic classification; Phylogenetic estimation; Self Organizing Map (SOM)

Indexed keywords

EID: 84885497521     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470669716.ch9     Document Type: Chapter

References (75)

1. Adams, M.D., Celniker, S.E., Holt, R.A., et al. (2000) The genome sequence of Drosophila melanogaster. Science, 287(5461), 2185-95.
2. Ahn, S.M., Kim, T.H., Lee, S., et al. (2009) The first Korean genome sequence and analysis:full genome sequencing for a socio-ethnic group. Genome Res, 19(9), 1622-9.
3. Ashkenasy, N., Sanchez-Quesada, J., Bayley, H., and Ghadiri, M.R. (2005) Recognizing a single base in an individual DNA strand: a step toward DNA sequencing in nanopores. Angew. Chem. Int. Ed. Engl., 44(9), 1401-4.
4. van Baren, M.J., Koebbe, B.C., and Brent, M.R. (2007) Using N-SCAN or TWINSCAN to predict gene structures in genomic DNA sequences. Curr Protoc Bioinformatics, Chapter 4, Unit 4.8.
5. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., et al. (2009) GenBank. Nucleic Acids Res., 37(Database issue), D26-31.
6. Bertone, P., Stolc, V., Royce, T.E., et al., (2004) Global identification of human transcribed sequences with genome tiling arrays. Science, 306(5705), 2242-6.
7. Birney, E., Stamatoyannopoulos, J.A., Dutta, A., et al., (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447(7146), 799-816.
8. Burge, C. and Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268(1), 78-94.
9. Burset, M. and Guigo, R. (1996) Evaluation of gene structure prediction programs. Genomics, 34(3), 353-67.
10. Carninci, P., Kasukawa, T., Katayama, S., et al. (2005) The transcriptional landscape of the mammalian genome. Science, 309(5740), 1559-63.
11. Chen, J.M., Cooper, D.N., Chuzhanova, N., et al. (2007) Gene conversion: mechanisms, evolution and human disease. Nat. Rev. Genet., 8(10), 762-75.
12. Cheng, J., Kapranov, P., Drenkow, J., et al. (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science, 308(5725), 1149-54.
13. Church, D.M., Goodstadt, L., Hillier, L.W., et al. (2009) Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol., 7(5), e1000112.
14. Clamp, M., Fry, B., Kamal, M., et al. (2007) Distinguishing protein-coding and noncoding genes in the human genome. Proc. Natl. Acad. Sci. U.S.A., 104(49), 19428-33.
15. Clark, A.G., Eisen, M.B., Smith, D.R., et al. (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature, 450(7167), 203-18.
16. Daub, J., Gardner, P.P., Tate, J., et al. (2008) The RNA WikiProject: community annotation of RNA families. RNA, 14(12), 2462-4.
17. Dunham, I., Shimizu, N., Roe, B.A., et al. (1999) The DNA sequence of human chromosome 22. Nature, 402(6761), 489-95.
18. Feuk, L., Carson, A.R., and Scherer, S.W. (2006) Structural variation in the human genome. Nat. Rev. Genet., 7(2), 85-97.
19. Finn, R.D., Tate, J., Mistry, J., et al. (2008) The Pfam protein families database. Nucleic Acids Res, 36(Database issue), D281-8.
20. Frazer, K.A., Ballinger, D.G., Cox, D.R., et al. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature, 449(7164), 851-61.
21. Gardner, P.P., Daub, J., Tate, J.G., et al. (2009) Rfam: updates to the RNA families database. Nucleic Acids Res., 37(Database issue), D136-40.
22. Griffiths-Jones, S., Saini, H.K., van Dongen, S., and Enright, A.J. (2008) MiRBase: tools for microRNA genomics. Nucleic Acids Res., 36(Database issue), D154-8.
23. Gstaiger, M. and Aebersold, R. (2009) Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat. Rev. Genet., 10(9), 617-27.
24. Guigo, R. and Reese, M.G. (2005) EGASP: collaboration through competition to find human genes. Nat. Methods, 2(8), 575-7.
25. Guigo, R., Flicek, P., Abril, J.F., et al., (2006) EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol., 7(Suppl 1), S2.
26. Guttman, M., Amit, I., Garber, M., et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 458(7235), 223-7.
27. Harrow, J., Denoeud, F., Frankish, A., et al. (2006) GENCODE: producing a reference annotation for ENCODE. Genome Biol., 7(Suppl 1), S4.
28. Hattori, M., Fujiyama, A., Taylor, T.D., et al. (2000) The DNA sequence of human chromosome 21. Nature, 405(6784), 311-19.
29. Hillier, L.W., Reinke, V., Green, P., et al. (2009) Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res., 19(4), 657-66.
30. Horton, R., Gibson, R., Coggill, P., et al. (2008) Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project. Immunogenetics, 60(1), 1-18.
31. Hsu, F., Kent, W.J., Clawson, H., et al. (2006) The UCSC Known Genes. Bioinformatics, 22(9), 1036-46.
32. Hubbard, T.J., Aken, B.L., Ayling, S., et al. (2009) Ensembl 2009. Nucleic Acids Res., 37(Database issue), D690-7.
33. Huss, J.W., Orozco, C., Goodale, J., et al. (2008) A gene Wiki for community annotation of gene function. PLoS Biol., 6(7), e175.
34. Iafrate, A.J., Feuk, L., Rivera, M.N., et al. (2004) Detection of large-scale variation in the human genome. Nat. Genet., 36(9), 949-51.
35. International HapMap Consortium (2003) The International HapMap Project. Nature, 426(6968), 789-96.
36. Jaillon, O., Aury, J.M., Brunet, F., et al. (2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature, 431(7011), 946-57.
37. Kapranov, P., Cawley, S.E., Drenkow. J., et al. (2002) Large-scale transcriptional activity in chromosomes 21 and 22. Science, 296(5569), 916-19.
38. Kent, W.J., Sugnet, C.W., Furey, T.S., et al. (2002) The human genome browser at UCSC. Genome Res., 12(6), 996-1006.
39. Kozak, M. (1984) Point mutations close to the AUG initiator codon affect the efficiency of translation of rat preproinsulin in vivo. Nature, 308(5956), 241-6.
40. Kulikova, T., Akhtar, R., Aldebert, P., et al. (2007) EMBL nucleotide sequence database in 2006. Nucleic Acids Res., 35(Database issue), D16-20.
41. Lander, E.S., Linton, L.M., Birren, B., et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409(6822), 860-921.
42. Lemons, D. and McGinnis, W. (2006) Genomic evolution of Hox gene clusters. Science, 313(5795), 1918-22.
43. Levy, S., Sutton, G., Ng, P.C., et al. (2007) The diploid genome sequence of an individual human. PLoS Biol., 5(10), e254.
44. Lin, M.F., Deoras, A.N., Rasmussen, M.D., and Kellis, M. (2008) Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes. PLoS Comput. Biol., 4(4), e1000067.
45. Liolios, K., Tavernarakis, N., Hugenholtz, P., and Kyrpides, N.C., (2006) The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Res., 34(Database issue), D332-4.
46. Matlin, A.J., Clark, F., and Smith, C.W. (2005) Understanding alternative splicing:towards a cellular code. Nat. Rev. Mol. Cell. Biol., 6(5), 386-98.
47. Morin, R., Bainbridge, M., Fejes, A., et al. (2008) Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. BioTechniques, 45(1), 81-94.
48. Mortazavi, A., Williams, B.A., McCue, K., et al. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods, 5(7), 621-8.
49. Mudge, J.M., Armstrong, S.D., McLaren, K., et al. (2008) Dynamic instability of the major urinary protein gene family revealed by genomic and phenotypic comparisons between C57 and 129 strain mice. Genome Biol., 9(5), R91.
50. Ponting, C.P., Oliver, P.L., and Reik, W. (2009) Evolution and functions of long noncoding RNAs. Cell, 136(4), 629-41.
51. Pruitt, K.D., Tatusova, T., and Maglott, D.R. (2005) NCBI Reference Sequence (Ref-Seq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 33(Database issue), D501-4.
52. Pruitt, K.D., Harrow, J., Harte, R.A., et al. (2009) The consensus coding sequence (CCDS) project: identifying a common protein-coding gene set for the human and mouse genomes. Genome Res., 19(7), 1316-23.
53. Rinn, J.L., Kertesz, M., Wang, J.K., et al. (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell, 129(7), 1311-23.
54. Schuster, S.C. (2008) Next-generation sequencing transforms today’s biology. Nat. Methods, 5(1), 16-18.
55. Sebat, J., Lakshmi, B., Troge, J., et al. (2004) Large-scale copy number polymorphism in the human genome. Science, 305(5683), 525-8.
56. Shiraki, T., Kondo, S., Katayama, S., et al. (2003) Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc. Natl. Acad. Sci. U.S.A., 100(26), 15776-81.
57. Stanke, M., Tzvetkova, A., and Morgenstern, B. (2006) AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome. Genome Biol., 7(Suppl 1), S11-18.
58. Stark, A., Lin, M.F., Kheradpour, P., et al. (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature, 450(7167), 219-32.
59. Sugawara, H., Ogasawara, O., Okubo, K., et al. (2008) DDBJ with new system and face. Nucleic Acids Res., 36(Database issue), D22-4.
60. Sultan, M., Schulz, M.H., Richard, H., et al. (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science, 321(5891), 956-60.
61. Suyama, M., Harrington, E., Bork, P., and Torrents, D. (2006) Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse genomes. PLoS Comput. Biol., 2(6), e76.
62. Toll-Riera, M., Bosch, N., Bellora, N., et al. (2009) Origin of primate orphan genes: a comparative genomics approach. Mol. Biol. Evol., 26(3), 603-12.
63. UniProt Consortium (2009) The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res., 37(Database issue), D169-74.
64. Velculescu, V.E., Zhang, L., Vogelstein, B., and Kinzler, K.W. (1995) Serial analysis of gene expression. Science, 270(5235), 484-7.
65. Venter, J.C., Adams, M.D., Myers, E.W., et al. (2001) The sequence of the human genome. Science, 291(5507), 1304-51.
66. Wang, E.T., Sandberg, R., Luo, S., et al. (2008a) Alternative isoform regulation in human tissue transcriptomes. Nature, 456(7221), 470-6.
67. Wang, J., Wang, W., Li, R., et al. (2008b) The diploid genome sequence of an Asian individual. Nature, 456(7218), 60-5.
68. Wang, Z. and Burge, C.B. (2008) Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA, 14(5), 802-13.
69. Wang, Z., Gerstein, M., and Snyder, M. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet., 10(1), 57-63.
70. Wheeler, D.A., Srinivasan, M., Egholm, M., et al. (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature, 452(7189), 872-6.
71. Willingham, A.T. and Gingeras, T.R. (2006) TUF love for “junk” DNA. Cell, 125(7), 1215-20.
72. Wilming, L.G., Gilbert, J.G., Howe, K., et al. (2008) The vertebrate genome annotation (Vega) database. Nucleic Acids Res., 36(Database issue), D753-60.
73. Wortman, J.R., Gilsenan, J.M., Joardar, V., et al. (2009) The 2008 update of the Aspergillus nidulans genome annotation: a community effort. Fungal Genet. Biol., 46(Suppl 1), S2-13.
74. Zhang, Z., Carriero, N., Zheng, D., et al. (2006) PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics, 22(12), 1437-9.
75. Zheng, D., Frankish, A., Baertsch, R., et al. (2007) Pseudogenes in the ENCODE regions:consensus annotation, analysis of transcription, and evolution. Genome Res., 17(6), 839-51.