Public access to the VirHostNet knowledge base is available at http://pbildb1.univ-lyon1.fr/virhostnet. Access can be made either anonymously (by default) or by creating a personal account (register in the account menu). On simple request, this personal account allows users to participate to the literature-curation effort. Literaturecurated and Database-curated protein-protein interactions flat files are available in a tabulated format on request. Contact V.N. (navratil@univ-lyon-1.fr) for more information. Figure 5 . VirHostNet Visualisator. Graph representation of the mTOR-infection network is drawn (right of the applet). Only interacting proteins of the mTOR pathway are represented (cellular proteins = blue nodes; host-host protein-protein interactions = blue edges). Viral interacting proteins are also added to define the infection network (viral proteins = coloured nodes according to viral taxonomy; virus-host protein-protein interactions = red edges). Cellular proteins of the network targeted by at least one viral protein (red stroke) are highlighted. The width of the edges is roughly proportional to the number of PMIDs used to describe the interaction. The width of the nodes is roughly proportional to the cellular degree, i.e. the number of cellular partners in the whole network. The taxonomical classification of viral proteins interacting with the mTOR network is given (left panel of the applet). The menu of the applet (top of the applet) allows users to define nodes and edges preferences (width, colour, labelling), interaction filtering (according to the number of methods, number of PMIDs or both), network navigation (expand viral or host neighbours) and graph layout. To obtain this figure, from the list of the 89 selected protein-protein interactions obtained in Figure 4E , users have to click on 'visualize' button. Then from the applet, in picking mode, they have to select all proteins and ask for viral proteins neighbours (in expand menu). Rfam: updates to the RNA families database Rfam is a collection of RNA sequence families, represented by multiple sequence alignments and covariance models (CMs). The primary aim of Rfam is to annotate new members of known RNA families on nucleotide sequences, particularly complete genomes, using sensitive BLAST filters in combination with CMs. A minority of families with a very broad taxonomic range (e.g. tRNA and rRNA) provide the majority of the sequence annotations, whilst the majority of Rfam families (e.g. snoRNAs and miRNAs) have a limited taxonomic range and provide a limited number of annotations. Recent improvements to the website, methodologies and data used by Rfam are discussed. Rfam is freely available on the Web at http://rfam.sanger.ac.uk/and http://rfam.janelia.org/. Rfam is a database of sequence families of structural RNAs, including non-coding RNA genes as well as cisregulatory RNA elements. Rfam release 9.0 contains 603 families, each represented by a multiple sequence alignment of known and predicted representative members of the family, annotated with a consensus base-paired secondary structure. This so-called SEED alignment is used to build a covariance model (CM) with the Infernal software (1) . Each Rfam covariance model is searched against a nucleotide sequence database, producing a list of putative hits. Matches that score above a curated threshold are then aligned to the CM to produce a so-called FULL alignment. This process is outlined diagrammatically in Figure 1 . The Rfam database was developed as a generic approach to the annotation of structured RNA families on genomic sequences (2, 3) , but it has been widely used as a source of reliable alignments and structures for the purposes of training and benchmarking RNA sequence and secondary structure analysis software.