There have been several significant improvements to the comparative genomics resources in WormBase. Building on the use of Ensembl technology (10
) WormBase now displays orthologous genes found in many of the vertebrate species included in Ensembl such as human (11 801) and mouse (12 141). There are several other methods for determining orthologous relationships between genes in different species and the different methods do not always agree. Rather than selecting a single method of ortholog determination, WormBase has chosen to represent a selection of methods and let the user decide. To this end, homology groups are also included from InParanoid (12
), NCBI-KOGS (13
), TreeFam (14
), OrthoMCL (15
) as well as one-off analyses (16
) and individual user contributions.
The Compara system that is used to calculate these orthologs and paralogs also determines syntenic regions between the more closely related Caenorhabditis species (currently elegans, briggsae, remanei and brenneri). These alignments are used to drive a recently developed synteny viewer (), which is accessible via a new link in the main navigation bar at the top of each page. Users can scroll and zoom around the genome as with the main Genome Browser, change which genome is to act as the reference and follow links to genes shown.
Syntenic alignments of C. elegans, C. briggsae and C. remanei.
We now manually curate C. briggsae gene predictions in response to user queries. Genome-wide experiments in C. briggsae are also being included with the addition of 42 500 SNPs identified by the Washington University SNP Research Facility which are used to generate a genetic map.
To make it easier for users to explore differences in gene structure between species, we have added a new track to the Genome Browser showing the alignment of cDNA data from other Caenorhabditis
species to the elegans
genome. This complements the existing tracks where cDNAs from C. elegans
itself are separated from those of all other nematodes. This track gives a quick overview of the level of conservation between the various Caenorhabditis
species. The species from which the cDNA derives is indicated as a mouse-over tool tip. As the genome sequences of the other Caenorhabditis
are annotated and integrated, genome browsers will be established with similar tracks of cDNA alignments where possible. The latest species added to the genome browser is Brugia malayi
), sequenced by TIGR and we expect to be adding an updated C. remanei
genome plus new browsers for C. brenneri
and Caenorhabditis japonica
) in the near future. In addition, WormBase is actively working with the Nematode Genome Annotation Assessment Project (nGASP) (www.wormbase.org/wiki/index.php/Gene_Prediction
) to determine, display and maintain a canonical gene set for each species.