BMC Genomics 2006, 7:300 http://www.biomedcentral.com/1471-2164/7/300 The system provides an integrated BLASTP [14] search and is able to link the sequences in the BLAST database with the records in the SQL database via an ID. Thus the user can, apart from the sequence, immediately access all related information. The organization of the database lends itself to different types of statistical analysis. For each protein, a set of tables and graphs can be generated. These analyses provide important information for the comparison of the protein inventory of specific taxa and species, as well as important insights into the selected pro- tein superfamily. The protein inventory table gives an overview about the class distribution and the number of class members of all or a number of selected species (ordered by taxonomy). Color-coding of the cells helps to quickly identify characteristic patterns of specific taxa. Charts show the ratio of protein classes and the distribu- tion of the molecular weight for a chosen set of classes. All charts are generated on the fly in resolution-independent SVG-code, so they can also be used for print. Future developments Pfarao provides a solid platform for additional features and significant future developments of the system are underway. The front end will be extended to allow the graphical representation and fast browsing of large align- ments of selected sequences that will be of great value for mutational studies. The interface is also intended to sup- port the generation of phylogenetic trees for a user- defined set of sequences. These extensions will increase the transparency of the manual annotation process, as the user will be able to look at the two basic sources of infor- mation about protein sequence relations. It is also planned to incorporate the corresponding DNA data and to track the various alternative splice forms of the pro- teins. Case study Pfarao has initially been developed for cytoskeletal and motor proteins but can easily been adapted to any pro- tein. The database for cytoskeletal and motor proteins is called CyMoBase [23]. Our current in house database con- tains 3265 Sequences (3095759 amino acids) from 666 species, 494 publications, and 385 references to 165 sequencing projects but is being extended on a daily basis. A portion of the data has been released in the publicly available CyMoBase. Conclusion Here, we introduce a web application for the analysis of proteins from manual annotation and their relationship. The major motivation for this work was to provide an integrated environment that organizes and relates all rele- vant information and presents it using a high quality interface. Pfarao is a tool that allows the researcher to con- stantly monitor the state of the work without having to manually aggregate data from a range of sources. It has been developed for the analysis of cytoskeletal and motor proteins (CyMoBase) but can easily be customized for any type of protein. Availability and requirements CyMoBase can be accessed at http://www.motorpro tein.de/cymobase. Due to the technologies used, it requires Firefox version 1.5 or greater with cookies and JavaScript enabled. Other browsers do not have the required feature set or do not comply with the standards of the W3C [19]. The database schema, the web application, the server program and all scripts can be obtained upon request and used under a Creative Commons License. Use of Pfarao by non-aca- demics requires permission. Abbreviations ID Identification Number SVG Scalable Vector Graphics XHTML Extensible HyperText Markup Language XML Extensible Markup Language XML-RPC Extensible Markup Language – Remote Proce- dure Call Authors' contributions MK specified the requirements from a users perspective, defined the rules for data handling and participated in the design of the interface. He collected all the data and eval- uated every function of the system. FO carried out the implementation of the system, designed the database scheme and did the technical design and the program- ming. Both authors wrote and approved the final manu- script. Additional material Additional File 1 The file contains the detailed database schema. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-7-300-S1.pdf] Acknowledgements M.K. is supported by a Liebig Stipendium of the Fonds der Chemischen Industrie, which is in part financed by the BMBF. This work has been funded by grant I80798 of the VolkswagenStiftung. Page 7 of 8 (page number not for citation purposes)