C. elegans ORFeome version 3.1: Increasing the coverage of ORFeome resources with improved gene predictions

Genome Research

Volumn 14, Issue 10 B, 2004, Pages 2064-2069

  Lamesch, Philippe ^a,b   Milstein, Stuart ^a   Hao, Tong ^a   Rosenberg, Jennifer ^a   Li, Ning ^a   Sequerra, Reynaldo ^c   Bosak, Stephanie ^c   Doucette Stamm, Lynn ^c   Vandenhaute, Jean ^b   Hill, David E ^a   Vidal, Marc ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF NAMUR   (Belgium)

^c Agencourt Bioscience Corporation   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

ACCURACY; ARTICLE; CAENORHABDITIS ELEGANS; COMPUTER PROGRAM; CONTROLLED STUDY; DNA LIBRARY; EXON; GENE AMPLIFICATION; GENE STRUCTURE; GENETIC CODE; GENOME ANALYSIS; INTRON; MOLECULAR CLONING; NONHUMAN; OPEN READING FRAME; POLYMERASE CHAIN REACTION; PREDICTION; PRIORITY JOURNAL; VALIDATION PROCESS;

CAENORHABDITIS; CAENORHABDITIS ELEGANS;

EID: 7444220617     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.2496804     Document Type: Article

References (18)

1. Blumenthal, T., Evans, D., Link, C.D., Guffanti, A., Lawson, D., Thierry-Mieg, J., Thierry-Mieg, D., Chiu, W.L., Duke, K., Kiraly, M., et al. 2002. A global analysis of Caenorhabditis elegans operons. Nature 417: 797-798.
2. Burset, M. and Guigo, R. 1996. Evaluation of gene structure prediction programs. Genomics 34: 353-367.
3. The C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282: 2012-2018.
4. Cliften, P.F., Hillier, L.W., Fulton, L., Graves, T., Miner, T., Gish, W.R., Waterston, R.H., and Johnston, M. 2001. Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res. 11: 1143-1144.
5. Cliften, P., Sudarsanam, P., Desikan, A., Fulton, L., Fulton, B., Majors, J., Waterston, R., Cohen, B.A., and Johnston, M. 2003. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301: 71-76.
6. Hartley, J.L., Temple, G.F., and Brasch, M.A. 2000. DNA cloning using in vitro site-specific recombination. Genome Res. 10: 1788-1795.
7. Hild, M., Beckmann, B., Haas, S.A., Koch, B., Solovyev, V., Busold, C., Fellenberg, K., Boutros, M., Vingron, M., Sauer, F., et al. 2003. An integrated annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome. Genome Biol. 5: R3.
8. Hillier, L. and Green, P. 1991. OSP: A computer program for choosing PCR and DNA sequencing primers. PCR Methods Appl. 1: 124-128.
9. Kellis, M., Patterson, N., Endrizzi, M., Birrent, B., and Lander, E.S. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 233-234.
10. Korf, I., Flicek, P., Duan, D., and Brent, M.R. 2001. Integrating genomic homology into gene structure prediction. Bioinformatics 17: 140-148.
11. Reboul, J., Vaglio, P., Tzellas, N., Thierry-Mieg, N., Moore, T., Jackson, C., Shin-I, T., Kohara, Y., Thierry-Mieg, D., Thierry-Mieg, J., et al. 2001. Open-reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans. Nat. Genet. 27: 332-336.
12. Reboul, J., Vaglio, P., Rual, J.F., Lamesch, P., Martinez, M., Armstrong, C.M., Li, S., Jacotot, L., Bertin, N., Janky, R., et al. 2003. C. elegans ORFeome version 1.1: Experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat. Genet. 34: 35-41.
13. Stein, L., Sternberg, P., Durbin, R., Thierry-Mieg, J., and Spieth, J. 2001. WormBase: Network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Res. 29: 82-86.
14. Stein, L.D., Bao, Z., Blasiar, D., Blumenthal, T., Brent, M.R., Chen, N., Chinwalla, A., Clarke, L., Clee, C., Coghlan, A., et al. 2003. The genome sequence of Caenorhabditis briggsae: A platform for comparative genomics. PloS Biol. 1: E45.
15. Vaglio, P., Lamesch, P., Reboul, J., Rual, J.-F., Martinez, M., Hill, D., and Vidal, M. 2003. WorfDB: The Caenorhabitis elegans ORFeome Database. Nucleic Acids Res. 31: 237-240.
16. Walhout, A.J., Sordella, R., Lu, X., Hartley, J.L., Temple, G.F., Brasch, M.A., Thierry-Mieg, N., and Vidal, M. 2000a. Protein interaction mapping in C. elegans using proteins involved in vulval development. Science 287: 116-122.
17. Walhout, A.J., Temple, G.F., Brasch, M.A., Hartley, J.L., Lorson, M.A., van den Heuvel, S., and Vidal, M. 2000b. Gateway recombinational cloning: Application to the cloning of large numbers of open reading frames or ORFeomes. Methods Enzymol. 328: 575-592.
18. Yamada, K., Lim, J., Dale, J.M., Chen, H., Shinn, P., Palm, C.J., Southwick, A.M., Wu, H.C., Kim, C., Nguyen, M., et al. 2003. Empirical analysis of the transcriptional activity in the Arabidopsis genome. Science 302: 842-846.