WormBase 2007

Abstract

WormBase (www.wormbase.org) is the major publicly available database of information about Caenorhabditis elegans, an important system for basic biological and biomedical research. Derived from the initial ACeDB database of C. elegans genetic and sequence information, WormBase now includes the genomic, anatomical and functional information about C. elegans, other Caenorhabditis species and other nematodes. As such, it is a crucial resource not only for C. elegans biologists but the larger biomedical and bioinformatics communities. Coverage of core areas of C. elegans biology will allow the biomedical community to make full use of the results of intensive molecular genetic analysis and functional genomic studies of this organism. Improved search and display tools, wider cross-species comparisons and extended ontologies are some of the features that will help scientists extend their research and take advantage of other nematode species genome sequences.

A Comprehensive Review of Emerging Computational Methods for Gene Identification

“…Meanwhile, the multiple genome alignments between C. elegans, C. briggsae, and C. remanei, and the alignments of ESTs, mRNAs, and proteins with the C. elegans genome were provided as additional data for different types of methods [9]. The reference gene sets were derived from WormBase [151,152] and were used as benchmarks to measure the results of different programs. The RNA-Seq Genome Annotation Assessment Project (RGASP) Consortium [153] conducted the comprehensive assessment for the construction of transcripts.…”

Integrating Bioinformatics and Computational Biology: Perspectives and Possibilities for In Silico Network Reconstruction in Molecular Systems Biology

“…In such charts, the individual function of a protein is superimposed onto the particular steps where that protein is active. An example where genome annotation has been used to reconstruct the full complement of metabolic pathways for Lactobacillus plantarum can be found in [45,49]. Sequence based annotation is not possible when a new gene is not homologous to any gene of known function.…”

“…The NCBI web pages [36][37][38][39][40][41][42] and the KEGG web pages [43][44][45][46][47] contain annotation information for most organisms with fully sequenced genomes. Expasy [48,49] also has this information with a focus on the proteins. The TIGR institute [50,51] web pages and the DOE Joint Genome Institute [52] web pages also contain much of this information.…”

Database of queryable gene expression patterns for Xenopus

“…For example, in model organism specific databases ZFin (Sprague et al, 2003), Wormbase (Rogers et al, 2008), MEPD (Henrich et al, 2005), Geisha (Bell et al, 2004;Darnell et al, 2007), GXD (Ringwald et al, 1997;Smith et al, 2007), BDGP (Tomancak et al, 2007), and Xenbase (Bowes et al, 2008), and across multiple species in VisiGene (Kuhn et al, 2007), 4DX-press (Haudry et al, 2008), and quickImage (Gilchrist et al, 2008). The general areas of bioimage informatics and related topics are covered in a recent review (Peng, 2008).…”