Generating the physical map of the Fugu genome: Development of computer system by using Java 2 Enter
By Tanya Vavouri
Ms, MRC-Human Genome Mapping Project Resource Centre, UK
The draft sequence of the Fugu genome is now publicly available on the Internet (http://fugu.hgmp.mrc.ac.uk/). It exists as 12,403 assembled sequences (scaffolds), varying in size between 2 and 650 Kbp. The scaffolds were generated using a whole genome shotgun approach by the International Fugu Sequencing Consortium. There is, howerver, no physical map of the Fugu genome. Our aim is to order the scaffolds and based on that, carry out the finishing of the genome.
We are developing an informatics computer system that uses experimental data to order the scaffolds based on data stored in a relational database (Sybase). The order of the scaffolds is interactively validated using the Apollo genome viewer which is a Java application developed by the Berkeley Drosophila Genome Centre and the Sanger Centre, for annotating genomic sequences. We have configured and integrated Apollo with our computer system to enable the display and interactive manipulation of ordered scaffolds. The Apollo-derived client application communicates with the relational database through a middle layer of Enterprise Java Beans (EJBs).
This project is currently in progress and is paving the way to produce a complete and finished Fugu genome.