Nucleic Acids Research, 2003, Vol. 31, No. 1 133-137
© 2003 Oxford University Press
WormBase: a cross-species database for comparative genomics
Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA 1 Howard Hughes Medical Institute and California Institute of Technology, Pasadena, CA, USA 2 The Sanger Centre, Hinxton, UK 3 Genome Sequencing Center, Washington University, St Louis, MO, USA
*To whom correspondence should be addressed. Fax: +1 516 367 8389; Email: lstein{at}cshl.org
ABSTRACT
WormBase (http://www.wormbase.org/) is a web-accessible central data repository for information about Caenorhabditis elegans and related nematodes. The past two years have seen a significant expansion in the biological scope of WormBase, including the integration of large-scale, genome-wide data sets, the inclusion of genome sequence and gene predictions from related species and active literature curation. This expansion of data has also driven the development and refinement of user interfaces and operability, including a new Genome Browser, new searches and facilities for data access and the inclusion of extensive documentation. These advances have expanded WormBase beyond the obvious target audience of C. elegans researchers, to include researchers wishing to explore problems in functional and comparative genomics within the context of a powerful genetic system.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  T. K. Means, E. Mylonakis, E. Tampakakis, R. A. Colvin, E. Seung, L. Puckett, M. F. Tai, C. R. Stewart, R. Pukkila-Worley, S. E. Hickman, et al. Evolutionarily conserved recognition and innate immunity to fungal pathogens by the scavenger receptors SCARF1 and CD36 J. Exp. Med., March 16, 2009; 206(3): 637 - 653. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Miyata, J. Begun, E. R. Troemel, and F. M. Ausubel DAF-16-Dependent Suppression of Immunity During Reproduction in Caenorhabditis elegans Genetics, February 1, 2008; 178(2): 903 - 918. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. He, J. Wang, T. Liu, X. S. Liu, T. Li, Y. Wang, Z. Qian, H. Zheng, X. Zhu, T. Wu, et al. Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray Genome Res., October 1, 2007; 17(10): 1471 - 1477. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Y. Kim and W. C. Hahn Cancer genomics: integrating form and function Carcinogenesis, July 1, 2007; 28(7): 1387 - 1392. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Deng, X. Zhu, G. Skogerbo, Y. Zhao, Z. Fu, Y. Wang, H. He, L. Cai, H. Sun, C. Liu, et al. Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression Genome Res., January 1, 2006; 16(1): 20 - 29. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. D. Wren, W. H. Hildebrand, S. Chandrasekaran, and U. Melcher Markov model recognition and classification of DNA/protein sequences within large text databases Bioinformatics, November 1, 2005; 21(21): 4046 - 4053. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. G. Fernandez, K. C. Gunsalus, J. Huang, L.-S. Chuang, N. Ying, H.-l. Liang, C. Tang, A. J. Schetter, C. Zegar, J.-F. Rual, et al. New genes with roles in the C. elegans embryo revealed using RNAi of ovary-enriched ORFeome clones Genome Res., February 1, 2005; 15(2): 250 - 259. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Bairoch, R. Apweiler, C. H. Wu, W. C. Barker, B. Boeckmann, S. Ferro, E. Gasteiger, H. Huang, R. Lopez, M. Magrane, et al. The Universal Protein Resource (UniProt) Nucleic Acids Res., January 1, 2005; 33(suppl_1): D154 - D159. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Chen, T. W. Harris, I. Antoshechkin, C. Bastiani, T. Bieri, D. Blasiar, K. Bradnam, P. Canaran, J. Chan, C.-K. Chen, et al. WormBase: a comprehensive data resource for Caenorhabditis biology and genomics Nucleic Acids Res., January 1, 2005; 33(suppl_1): D383 - D389. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Grabbe, C. G. Zervas, T. Hunter, N. H. Brown, and R. H. Palmer Focal adhesion kinase is not required for integrin function or viability in Drosophila Development, December 1, 2004; 131(23): 5795 - 5805. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Deplancke, D. Dupuy, M. Vidal, and A. J.M. Walhout A Gateway-Compatible Yeast One-Hybrid System Genome Res., October 1, 2004; 14(10b): 2093 - 2101. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 U. OHLER, S. YEKTA, L. P. LIM, D. P. BARTEL, and C. B. BURGE Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification RNA, September 1, 2004; 10(9): 1309 - 1322. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. WANG, J. KIMBLE, and M. WICKENS Tissue-specific modification of gld-2 mRNA in C. elegans: Likely C-to-U editing RNA, September 1, 2004; 10(9): 1444 - 1448. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. M. Zahler, J. D. Tuttle, and A. D. Chisholm Genetic Suppression of Intronic +1G Mutations by Compensatory U1 snRNA Changes in Caenorhabditis elegans Genetics, August 1, 2004; 167(4): 1689 - 1696. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Curwen, E. Eyras, T. D. Andrews, L. Clarke, E. Mongin, S. M.J. Searle, and M. Clamp The Ensembl Automatic Gene Annotation System Genome Res., May 1, 2004; 14(5): 942 - 950. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Stalker, B. Gibbins, P. Meidl, J. Smith, W. Spooner, H.-R. Hotz, and A. V. Cox The Ensembl Web Site: Mechanics of a Genome Browser Genome Res., May 1, 2004; 14(5): 951 - 955. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. M.J. Searle, J. Gilbert, V. Iyer, and M. Clamp The Otter Annotation System Genome Res., May 1, 2004; 14(5): 963 - 970. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. T. Liberati, K. A. Fitzgerald, D. H. Kim, R. Feinbaum, D. T. Golenbock, and F. M. Ausubel Requirement for a conserved Toll/interleukin-1 resistance domain protein in the Caenorhabditis elegans immune response PNAS, April 27, 2004; 101(17): 6593 - 6598. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Andachi Caenorhabditis elegans T-box genes tbx-9 and tbx-8 are required for formation of hypodermis and body-wall muscle in embryogenesis Genes Cells, April 1, 2004; 9(4): 331 - 344. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Nikolaidis and M. Nei Concerted and Nonconcerted Evolution of the Hsp70 Gene Superfamily in Two Sibling Species of Nematodes Mol. Biol. Evol., March 1, 2004; 21(3): 498 - 505. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Apweiler, A. Bairoch, C. H. Wu, W. C. Barker, B. Boeckmann, S. Ferro, E. Gasteiger, H. Huang, R. Lopez, M. Magrane, et al. UniProt: the Universal Protein knowledgebase Nucleic Acids Res., January 1, 2004; 32(90001): D115 - 119. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Hotelier, L. Renault, X. Cousin, V. Negre, P. Marchot, and A. Chatonnet ESTHER, the database of the {alpha}/{beta}-hydrolase fold superfamily of proteins Nucleic Acids Res., January 1, 2004; 32(90001): D145 - 147. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Nakao, M. Yoshihama, and N. Kenmochi RPG: the Ribosomal Protein Gene database Nucleic Acids Res., January 1, 2004; 32(90001): D168 - 170. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Ruiz, M. Rouard, L. M. Raboin, M. Lartaud, P. Lagoda, and B. Courtois TropGENE-DB, a multi-tropical crop information system Nucleic Acids Res., January 1, 2004; 32(90001): D364 - 367. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Yazaki, K. Kojima, K. Suzuki, N. Kishimoto, and S. Kikuchi The Rice PIPELINE: a unification tool for plant functional genomics Nucleic Acids Res., January 1, 2004; 32(90001): D383 - 387. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. C. Gunsalus, W.-C. Yueh, P. MacMenamin, and F. Piano RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects Nucleic Acids Res., January 1, 2004; 32(90001): D406 - 410. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. W. Harris, N. Chen, F. Cunningham, M. Tello-Ruiz, I. Antoshechkin, C. Bastiani, T. Bieri, D. Blasiar, K. Bradnam, J. Chan, et al. WormBase: a multi-species resource for nematode biology and genomics Nucleic Acids Res., January 1, 2004; 32(90001): D411 - 417. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Wylie, J. C. Martin, M. Dante, M. D. Mitreva, S. W. Clifton, A. Chinwalla, R. H. Waterston, R. K. Wilson, and J. P. McCarter Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes Nucleic Acids Res., January 1, 2004; 32(90001): D423 - 426. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Lavoie, F. Debeane, Q.-D. Trinh, J.-F. Turcotte, L.-P. Corbeil-Girard, M.-J. Dicaire, A. Saint-Denis, M. Page, G. A. Rouleau, and B. Brais Polymorphism, shared functions and convergent evolution of genes with sequences coding for polyalanine domains Hum. Mol. Genet., November 15, 2003; 12(22): 2967 - 2979. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Hennig, D. Groth, and H. Lehrach Automated Gene Ontology annotation for anonymous sequence data Nucleic Acids Res., July 1, 2003; 31(13): 3712 - 3715. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Zehetner OntoBlast function: from sequence similarities directly to potential functional annotations by ontology terms Nucleic Acids Res., July 1, 2003; 31(13): 3799 - 3803. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C.-S. Goh, N. Lan, N. Echols, S. M. Douglas, D. Milburn, P. Bertone, R. Xiao, L.-C. Ma, D. Zheng, Z. Wunderlich, et al. SPINE 2: a system for collaborative structural proteomics within a federated database framework Nucleic Acids Res., June 1, 2003; 31(11): 2833 - 2838. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K.-Z. Lee, A. Eizinger, R. Nandakumar, S. C. Schuster, and R. J. Sommer Limited microsynteny between the genomes of Pristionchus pacificus and Caenorhabditis elegans Nucleic Acids Res., May 15, 2003; 31(10): 2553 - 2560. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S.J. MCKAY, R. JOHNSEN, J. KHATTRA, J. ASANO, D.L. BAILLIE, S. CHAN, N. DUBE, L. FANG, B. GOSZCZYNSKI, E. HA, et al. Gene Expression Profiling of Cells, Tissues, and Developmental Stages of the Nematode C. elegans Cold Spring Harb Symp Quant Biol, January 1, 2003; 68(0): 159 - 170. [Abstract] [PDF]
|
|