Public Sigenae Contig Browser .

Information About Contig Browser

The Sigenae Contig Browser

The aim of the Sigenae Contig Browser software is to give a simple and rapid visual access to information related to assembly and similarity feature of EST contigs.

A bit of history

In 2002, the Sigenae team installed a first generation of EST contigs query and visualization tools. This tool was developed by the Genoplante-Info team. In 2004, because of the new needs expressed by our users and the available genomic data for several species of the project, we decided to search a new environment to present these data. After a study of different softwares, we decided to use the Ensembl code to build this new tool.

The prerequisites

To prerequisites we had were:

• it must be able to store and present genomic data,
• the tool set must be GLP licensed,
• there must be a large community of developers and users,
• it must enable many different kinds of queries for the users,
• it must have a nice look and feel.

What can of services does it provide to biologists?

It enables to select contigs using many criterias linked to the contig itself, to its ESTs or mRNA composition or to the contig alignment features (nucleic and proteic hits). It gives a synthetic graphical view of the contig composition and alignment features. It allows data extraction in various formats to process or analyze them with your own system.

And in fact what is a contig?

Do to the limitation of sequencing technics, genes (speaking about EST for example) have to be split before sequencing and rebuilt after. A contig is the result of this rebuilding process. A contig can be a single nucleic sequence (EST or mRNA) matching with no other, it is then named a singlet. Or it can be an assembly of nucleic sequences sharing common sub-sequences.

© 2008 INRA / WTSI / EBI.