BMC Genomics 2006, 7:300 http://www.biomedcentral.com/1471-2164/7/300 Other Databases Pubmed NCBI Pfam Sequencing Centers Automated Processes Build Taxonomic Tree Pfam Scan Version Protein Domains Database Sequence Publications FASTA File Sequence Alignment Delegation Server Projects Species Tax. Tree Web Application Web Front End BLAST Search FDiigagurraem1of main tables and linked resources Diagram of main tables and linked resources. The Database (blue) with the central sequence table (cyan), important associated tables (white) and connected systems are shown. Lines connecting tables depict table relations. Arrows depict flow of informa- tion. FASTA files containing sequence alignments are imported and exported using Ruby [16] scripts. The import function uses the BioRuby [17] library. Other databases are referenced via their IDs, which are used to generate hyperlinks to records on their web sites. Automated processes are started by a delegation server, which receives instructions from the database on insert or update of records. The automated processes write information into the database using Active Record. The frontend is generated using the Ruby on Rails [10] web application framework. linked with primary databases like GenBank or PubMed. To be useful for the specific protein community, whose members are expected to work in all biological and med- ical sub disciplines, the information of the database has to be presented in the most comprehensible way. Web interface Great attention has been paid to a versatile yet easy to use web interface. We think that accessibility and high quality representation is key to a productive usage of the system. Data can be entered and edited using a series of forms and lists. Relations are represented as pull-down menus. Pfarao encompasses a live web front end that is generated from the content of the database at each request and thus always reflects the current data, eliminating the need for manual updates. To browse the content of the database, the user selects a set of proteins and protein classes, and is then guided to refine the selection by choosing a set of specific taxa or species. Taxa and species can either be selected from tables containing specific subsets, or from a tree representation of the taxa and species that is gener- ated to match the protein and protein class selection. Taxa and species can be browsed and selected by expanding/ collapsing and including/excluding subsections of the tree, or by using shortcuts or auto-completion fields (Fig. 2). We consider the selection of specific species and taxa a key feature for comparative analyses of protein invento- ries and diversity (Fig. 2). Upon confirmation of the selection of protein and spe- cies, the system compiles a list of all sequences matching the specified criteria and presents it as a list grouped by species in taxonomic order. Additional data about the spe- cies like alternative names, links to sequencing centres and publications, as well as detailed information about the sequences including publications, comments, domain organization, and the sequence data, can selectively be shown or hidden (Fig. 3). Page 4 of 8 (page number not for citation purposes)