The Ensembl automatic gene annotation system

Genome Research

Volumn 14, Issue 5, 2004, Pages 942-950

  Curwen, Val ^a   Eyras, Eduardo ^a   Andrews, T Daniel ^a   Clarke, Laura ^a   Mongin, Emmanuel ^a   Searle, Steven M J ^a   Clamp, Michele ^b  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

ACCESS TO INFORMATION; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; COMPUTER INTERFACE; COMPUTER PREDICTION; COMPUTER PROGRAM; COMPUTER SYSTEM; DNA SEQUENCE; EUKARYOTE; EXPRESSED SEQUENCE TAG; GENE ASSIGNMENT; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC DATABASE; HUMAN; NONHUMAN; PRIORITY JOURNAL; PSEUDOGENE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SYSTEM ANALYSIS; TANDEM REPEAT; UNTRANSLATED REGION;

ANIMALS; ANOPHELES; AUTOMATION; CAENORHABDITIS; COMPUTATIONAL BIOLOGY; DNA; DNA, HELMINTH; EXPRESSED SEQUENCE TAGS; GENE DOSAGE; GENES; GENES, HELMINTH; GENES, INSECT; GENOME; GENOME, HUMAN; HELMINTH PROTEINS; HUMANS; INSECT PROTEINS; MICE; PREDICTIVE VALUE OF TESTS; PROTEINS; PSEUDOGENES; RATS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE; TANDEM REPEAT SEQUENCES; UNTRANSLATED REGIONS;

DANIO RERIO; EUKARYOTA;

EID: 2442707676     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1858004     Document Type: Article

References (33)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
2. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
3. Birney, E., Clamp, M., and Durbin, R. 2004. Genewise and genomewise. Genome Res. (this issue).
4. Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.C., Estreicher, A., Gasteiger, E., Martin, M.J., Michoud, K., O'Donovan, C., Phan, I., et al. 2003. The SWISS-PROT protein knowledgebase and its supplement TrEMBL, in 2003. Nucleic Acids Res. 31: 365-370.
5. Boguski, M.S., Lowe, T.M., and Tolstoshev, C.M. 1993. dbEST-Database for expressed sequence tags. Nat. Genet. 4: 332-333.
6. Burge, C. and Karlin, S. 1997. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268: 78-94.
7. Burset, M. and Guigo, R. 1996. Evaluation of gene structure prediction programs. Genomics 34: 353-367.
8. Cuff, J.A., Coates, G.M.P., Cutts, T.J.R., and Rae, M. 2004. The Ensembl computing architecture. Genome Res. (this issue).
9. Deloukas, P., Matthews, L.H., Ashurst, J., Burton, J., Gilbert, J.G., Jones, M., Stavrides, G., Almeida, J.P., Babbage, A.K., Bagguley, C.L., et al. 2001. The DNA sequence and comparative analysis of human chromosome 20. Nature 414: 865-871.
10. Down, T.A. and Hubbard, T.J.P. 2002. Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res. 12: 458-461.
11. Fyras, E., Caccamo, M., Curwen, V., and Clamp, M. 2004. ESTGenes: Alternative splicing from ESTs in Ensembl. Genome Res. (this issue).
12. Gaunt, M.W. and Miles, M.A. 2002. An insect molecular clock dates the origin of the insects and accords with paleontological and biogeographic landmarks. Mol. Biol. Evol. 19: 748-761.
13. Harris, T.W., Lee, R., Schwarz, E., Bradnam, K., Lawson, D., Chen, W., Blasier, D., Kenny, E., Cunningham, F., Kishore, R., et al. 2003. WormBase: A cross-species database for comparative genomics. Nucleic Acids Res. 31: 133-137.
14. Heilig, R., Eckenberg, R., Petit, J.-L., Fonknechten, N., Da Silva., C., Cattolico, L., Levy, M., Barbe, V., de Berardinis., V., Ureta-Vidal, A., et al. 2003. The DNA sequence and analysis of human chromosome 14. Nature 421: 601-607.
15. Hillier, L.W., Fulton, R.S., Fulton, L.A., Graves, T.A., Pepin, K.H., Wagner-McPherson, C., Layman, D., Maas, J., Jaeger, S., Walker, R., et al. 2003. The DNA sequence of human chromosome 7. Nature 424: 157-164.
16. Holt, R.A., Subramanian, G.M., Halpern, A., Sutton, G.G., Charlab, R., Nusskern, D.R., Wincker, P., Clark, A.G., Ribeiro, J.M.C., Wides, R., et al. 2002. The genome sequence of the malaria mosquito Anopheles gambiae. Science 298: 129-149.
17. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
18. Karolchik, D., Baertsch, R., Diekhans, M., Furey, T.S., Hinrichs, A., Lu, Y.T., Roskin, K.M., Schwartz, M., Sugnet, C.W., Thomas, D.J., et al. 2003. The UCSC Genome Browser Database. Nucleic Acids Res. 31: 51-54.
19. Kasprzyk, A., Keefe, D., Smedley, D., London, D., Spooner, W., Melsopp, C., Hammond, M., Rocca-Serra, P., Cox, T., and Birney, E. 2004. EnsMart: A generic system for fast and flexible access to biological data. Genome Res. 14: 160-169.
20. Kelso, J., Visagie, J., Theiler, G., Christoffels, A., Bardien, S., Smedley, D., Otgaar, D., Greyling, G., Jongeneel, C., McCarthy, M., et al. 2003. evoc: A controlled vocabulary for unifying gene expression data. Genome Res. 13: 1222-1230.
21. Kent, W.J. 2002. BLAT-The BLAST-like alignment tool. Genome Res. 12: 656-664.
22. Lowe, T.M. and Eddy, S.R. 1997. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964.
23. Mongin, E., Louis, C., Holt, R.A., Birney, E., and Collins, F.H. 2004. The Anopheles gambiae genome: An update. Trends Parasitol. 20: 49-52.
24. Mott, R. 1997. Est-genome: A program to align spliced DNA sequences to unspliced genomic DNA. Comput. Appli. Biosci. 13: 477-478.
25. Mungall, A.J., Palmer, S.A., Sims, S.K., Edwards, C.A., Ashurst, J.L., Wilming, L., Jones, M.C., Horton, R., Hunt, S.E., Scott, C.E., et al. 2003. The DNA sequence and analysis of human chromosome 6. Nature 425: 775-776.
26. Okazaki, Y., Furuno, M., Kasukawa, T., Adachi, J., Bono, H., Kondo, S., Nikaido, I., Osato, N., Saito, R., Suzuki, H., et al. 2002. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420: 563-573.
27. Potter, S.C., Clarke, L., Curwen, V., Keenan, S., Mongin, E., Searle, S.M.J., Stabenau, A., Storey, R., and Clamp, M. 2004. The Ensembl analysis pipeline. Genome Res. (this issue).
28. Pruitt, K.D., Katz, K.S., Sicotte, H., and Maglott, D.R. 2000. Introducing RefSeq and LocusLink: Curated human genome resources at the NCBI. Trends Genet. 16: 44-47.
29. Solovyev, V.V., Salamov, A.A., and Lawrence, C.B. 1995. Identification of human gene structure using linear discriminate functions and dynamic programming. In Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, 3: 367-375.
30. Stabenau, A., McVicker, G., Melsopp, C., Proctor, G., Clamp, M., and Birney, E. 2004. The Ensembl core software libraries. Genome Res. (this issue).
31. Stoesser, G., Sterk, P., Tuli, M.A., Stoehr, P.J., and Cameron, G.N. 1997. EMBL nucleotide sequence database. Nucleic Acids Res. 25: 7-14.
32. Waterston, R.H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J.F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An, P., et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
33. Wootton, J.C. and Federhen, S. 1996. Analysis of compositionally biased regions in sequence databases. Methods Enzymol. 266: 554-571.