Development and evaluation of an automated annotation pipeline and cDNA annotation system

Genome Research

Volumn 13, Issue 6 B, 2003, Pages 1542-1551

  Kasukawa, Takeya ^a,b   Furuno, Masaaki ^a   Nikaido, Itoshi ^a   Bono, Hidemasa ^a   Hume, David A ^c   Bult, Carol ^d   Hill, David P ^d   Baldarelli, Richard ^d   Gough, Julian ^e   Kanapin, Alexander ^f   Matsuda, Hideo ^g   Schriml, Lynn M ^h   Hayashizaki, Yoshihide ^a,i   Okazaki, Yasushi ^a   Quackenbush, John ^j  

^a RIKEN YOKOHAMA INSTITUTE   (Japan)

^b NTT CORPORATION   (Japan)

^c UNIVERSITY OF QUEENSLAND   (Australia)

^d JACKSON LABORATORY   (United States)

^e MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

^f EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^g OSAKA UNIVERSITY   (Japan)

^h NATIONAL INSTITUTES OF HEALTH   (United States)

ⁱ RIKEN   (Japan)

^j J CRAIG VENTER INSTITUTE   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

ACCURACY; ARTICLE; AUTOMATION; CONTROLLED STUDY; DNA SEQUENCE; GENE FUNCTION; GENE IDENTIFICATION; INFORMATION PROCESSING; INTERNET; MOLECULAR CLONING; NOMENCLATURE; PRIORITY JOURNAL; QUALITY CONTROL; SEQUENCE ANALYSIS;

ANIMALS; AUTOMATIC DATA PROCESSING; COMPUTATIONAL BIOLOGY; CONTIG MAPPING; DATABASES, GENETIC; DNA, COMPLEMENTARY; GENES; HUMANS; INFORMATION MANAGEMENT; MICE; QUALITY CONTROL; REFERENCE STANDARDS; SOFTWARE DESIGN; USER-COMPUTER INTERFACE;

EID: 0038349286     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.992803     Document Type: Article

References (20)

1. Adams, M.D., Celniker, S.E., Holt, R.A., Evans, C.A., Gocayne, J.D., Amanatides, P.G., Scherer, S.E., Li, P.W., Hoskins, R.A., Galle, R.F., et al. 2000. The genome sequence of Drosophila melanogaster. Science 287: 2185-2195.
2. 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.
3. Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Birney, E., Biswas, M., Bucher, P., Cerutti, L., Corpet, F., Croning, M.D., et al. 2001. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 29: 37-40.
4. Bairoch, A. and Apweiler, R. 2000. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28: 45-48.
5. Blake, J.A., Richardson, J.E., Bult, C.J., Kadin, J.A., and Eppig, J.T. 2002. The Mouse Genome Database (MGD): The model organism database for the laboratory mouse. Nucleic Acids Res. 30: 113-115.
6. Boguski, M.S. and Schuler, G.D. 1995. ESTablishing a human transcript map. Nat. Genet. 10: 369-371.
7. Boguski, M.S., Lowe, T.M., and Tolstoshev, C.M. 1993. dbEST - Database for "expressed sequence tags". Nat. Genet. 4: 332-333.
8. Bono, H., Kasukawa, T., Hayashizaki, Y., and Okazaki, Y. 2002. READ: RIKEN Expression Array Database. Nucleic Acids Res. 30: 211-213.
9. Bono, H., Yagi, K., Kasukawa, T., Nikaido, I., Tominaga, N., Miki, R., Mizuno, Y., Tomaru, Y., Goto, H., Nitanda, H., et al. 2003. Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays. Genome Res. (this issue).
10. Carninci, P., Waki, K., Shiraki, T., Konno, H., Shibata, K., Itoh, M., Aizawa, K., Arakawa, T., Ishii, Y., Sasaki, D., et al. 2003. Targeting a complex transcriptome: The construction of the mouse full-length cDNA encyclopedia. Genome Res. (this issue).
11. The FANTOM Consortium and the RIKEN Genome Exploration Research Group Phase I and II Team. 2002. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420: 563-573.
12. The Gene Ontology Consortium. 2001. Creating the gene ontology resource: Design and implementation. Genome Res. 11: 1425-1433.
13. Gordon, D., Abajian, C., and Green, P. 1998. Consed: A graphical tool for sequence finishing. Genome Res. 8: 195-202.
14. Gough, J., Karplus, K., Hughey, R., and Chothia, C. 2001. Assignment of homology to genorne sequences using a library of hidden Markov models that represent all proteins of known structure. J. Mol. Biol. 313: 903-919.
15. Kawaji, H., Schonbach, C., Matsuo, Y., Kawai, J., Okazaki, Y., Hayashizaki, Y., and Matsuda, H. 2002. Exploration of novel motifs derived from mouse cDNA sequences. Genome Res. 12: 367-378.
16. Pearson, W.R., Wood, T., Zhang, Z., and Miller, W. 1997. Comparison of DNA sequences with protein sequences. Genomics 46: 24-36.
17. Pruitt, K.D. and Maglott, D.R. 2001. RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res. 29: 137-140.
18. Quackenbush, J. 2000. Viva la revolution! A report from the FANTOM meeting. Nat. Genet. 26: 255-256.
19. Quackenbush, J., Cho, J., Lee, D., Liang, F., Holt, I., Karamycheva, S., Parvizi, B., Pertea, G., Sultana, R., and White, J. 2001. The TIGR Gene Indices: Analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res. 29: 159-164.
20. Wu, C.H., Huang, H., Arminski, L., Castro-Alvear, J., Chen, Y., Hu, Z.Z., Ledley, R.S., Lewis, K.C., Mewes, H.W., Orcutt, B.C., et al. 2002. The Protein Information Resource: An integrated public resource of functional annotation of proteins. Nucleic Acids Res. 30: 35-37.