"Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quiet diverse. RNAbrowse is an user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details.
The massive sequencing cost decrease has attracted a large community of new users, some of them studying organisms for which the reference genome sequence is still not available. When trying to understand mechanisms taking place at the gene level they usually would start with a de novo transcriptome assembly approach. Software packages such as Trinity or Oases are mature enough to produce reliable contigs from short reads. The analyses performed on the assembled contigs generate a large amount of heterogeneous results including variations, functional annotation and expression measurements. The processing steps of these pipelines are usually shared inside the community but the parameters, the tools and the reference databases used are specific. The results are often provided throught a WEB server including a BLAST query form and download links.
Cbrowse is a WEB environment presenting this kind of results throught graphical views and query forms. The functional annotation part is not implemented yet and the query possibilities are very limited. The Galaxy engine provides users with an interface to create and track workflow executions. It already embeds RNA-Seq analysis and assembly components. However, none of them offers user-friendly query and vizualisation features designed for RNA-Seq de novo annotation.
In its last version (0.8), biomart is developed as an easily extensible query infrastructures which can be specialized in the presentation of focused data types. On top of the database and beside the proposed query forms it is possible to add new pages as plug-ins in order to present data in a user-friendly way.
RNAbrowse permits sequencing facilities and, even small, bioinformatic teams to give a user-friendly access to RNA-Seq de novo results, helping biologists to analyse and extract meaningful information from their data. RNAbrowse includes two components: a web-based user interface and an administration command line tool presented here-after.