International Mammalian Genome Society

B11 Tools for EST Mapping

Patricia Rodriguez-Tome. Wellcome Trust Genomic Center, Cambridge, UK

Expressed Sequence Tags (ESTs) are cheap, easy and quick to obtain and sample many genes. They are very useful for developing Sequence Tags Sites (STSs) for mapping. However ESTs have many problems and the public EST databases contain all the errors and high redundancy intrinsic to the submitted data. It is often necessary to provide derived views as a better starting point for research.

To help a Mouse European Consortium to build their Radiation Hybrid maps, we have developed a set of tools that help chose the relevant ESTs for mapping:

• Alignment and cluster databases offer derived views of the data, grouping the ESTs that are similar and thus removing part of the redundancy problems (JESAM package).(http://corba.ebi.ac.uk/EST)
• An allocation database (RHalloc) allows the managment of the project. (http://corba.ebi.ac.uk/RHdb/RHalloc)
• Data is submitted to RHdb, the public repository for Radiation Hybrid data, which in turns offers public access. (http://www.ebi.ac.uk/RHdb)
• Various programs, installed on the user site, access those databases through the Internet and allow comparison between the working data and public data.
• WWW pages and Java clients offer the browsing and query interfaces to all these databases.

All the software and databases are published to the Internet with CORBA interfaces to enable flexible global access to the data and services for EST mapping at the EBI.

For more information on the CORBA developments at the EBi please visit http://corba.ebi.ac.uk.