From EST sequences to Radiation Hybrid Maps
by Jeremy Parsons and Patricia Rodriguez-Tomé
EMBL Outstation - Hinxton, the European Bioinformatics Institute,
Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Whole genome radiation hybrid (RH) mapping provides a means to localise any Sequence Tagged Site (STS), i.e. EST, genetic marker, or other genomic fragment, to a defined map position in the genome, via the polymerase chain reaction (PCR). In 1995, a database - the Radiation Hybrid database (RHdb, Tome et al., 1997) was set up at the EBI to maintain the results of such PCR experiments including, at that time, an international consortium working on the human genome. Now, with the availability of RH panels for the mouse genome (T31, McCarthy et al. 1997), and large-scale mouse EST sequencing it is possible to build a catalogue of mapped mouse genes. To make the mapping efficient it is important to avoid effort wasted on mapping cognate sequences multiple times.
At the EBI we have implemented a complete workbench for mouse RH mapping :
- EST clusteringRedundancy within the EST databases is discovered by superclustering all known mouse mRNA sequences together. The cluster database and the progenitor alignment/overlap and sequence databases are all offered with CORBA interfaces and Java clients allowing access from anywhere in the world.
To assist in international cooperation, a database has been set up to help organise the EST allocations between groups. This database feeds off the supercluster information.
The radiation hybrid database offers a centralised site where all raw data information can be found. Statistics on the data are calculated daily and shown on the web pages. Java applets act as clients to access the information in a user-friendly way. All these services are offered by public CORBA servers and the underlying software is portable and free.
Nothing in this workbench is species specific. Clusters are being prepared for both Rat and Zebrafish. Others species will follow depending on the interest from the user community.
Article by: Jeremy Parsons and Patricia Rodriguez-Tomé
Resources and further information
European Bioinformatics Institute (EMBL-EBI)CORBA (servers) at the EBI
RHdb -- Radiation Hybrid Database
- RHalloc -- EST allocation between groups
External sites are not endorsed by EMBL-EBI