S T A R S

Sequence Typing Analysis and Retrieval System

by Man-Suen Chan and Nicki Ventress, Copyright University of Oxford 2001

Using STARS for the first time STARS is an alternative interface to staden for sequence assembly for sequence typing projects. Sequence typing projects typically involve the sequencing of the same gene, or gene fragment, many times in order to determine polymorphisms. The standard staden interfaces, pregap4 and gap4,are more suited to assembling long contigs. The STARS interface, on the other hand has been designed with sequence typing projects in mind and allows the assembly of large numbers of short contigs into the same database. These contigs can be retrieved and edited from the interface using a standard staden contig editor. The system also performs user logging etc and can therefore be used as a lab database for your projects. The software was initially designed for managing sequencing projects using Multi Locus Sequence Typing (MLST) of bacteria.

Acknowledgements
Users' Guide
Administrators' Guide
Note added 17th December 2008
STARS was originally written in 2001 for the bioinformatics servers at the University of Oxford running the Solaris operating system. The original developers are now in other employment and are no longer supporting or developing STARS as part of their work. The recommended route for obtaining STARS is now the biolinux project run by the NERC Environmental Bioinformatics Centre in Oxford ( http://nebc.nox.ac.uk/biolinux.html). This is a customised distribution of linux for bioinformatics which incorporates staden and STARS as part of the distribution. If you wish to use STARS you should contact the NEBC through their website. Official support is only available to NERC staff but there is a discussion list for community support ( http://nebc.nox.ac.uk/mailman/listinfo/bio-linux ). The original software is still available through sourceforge (http://sourceforge.net/projects/stars/ ) but is no longer supported.
For specific groups of users there is additional support. For those interested in using STARS for Multi Locus Sequence Typing of bacteria informal advice is available from Keith Jolley at the Department of Zoology, University of Oxford ( keith.jolley@zoo.ox.ac.uk ). For users at the University of Oxford the STARS software is installed and supported on the servers of the Computational Biology Research Group ( http://www.cbrg.ox.ac.uk ).