genes that can be assessed either via pathways or directly from the ‘PROTEINS’ menu. In the process of manual data curation, we collected the available information con- cerning alternative gene and protein names and amino acid sequences available in the NCBI databases (22), 3D structures available in the protein data bank (23) and various features available in other databases (e.g. infor- mation about the enzymatic function, presence of isoforms, cellular/tissue and subcellular localization, together with links to the relevant database entries). Currently the DNA repair protein data set encompasses only E. coli, S. cerevisiae and H. sapiens, but will be expanded in the future and may eventually comprise all orthologs of the functionally characterized enzymes iden- tiﬁable in fully sequenced genomes. DISEASES: Thus far, we have compiled information about 40 diseases caused by the mutations in 32 genes linked to defects in DNA repair proteins. This data set is presented as a table with hyperlinks to the proteins con- cerned, and to the relevant entries in the Online Mendelian Inheritance in Man (OMIM) database (22). Each disease has its own subpage with a succinct description and add- itional links (e.g. keywords). Reciprocal links to diseases are also available in each protein ﬁeld. KEYWORDS: This menu provides quick access to the most common keywords used to annotate the database entities according to biological processes and activities such as: DNA repair pathways, the response to DNA damage, the cell cycle checkpoint control, the DNA N-glycosylase, the DNA N-glycosylase/AP-lyase, etc. PUBLICATIONS: Literature references to entries in the PubMed database (22) have been compiled into an additional data set, currently comprising 2613 positions. IMPLEMENTATION REPAIRtoire has been implemented using the Django web framework (http://www.djangoproject.com/). It uses a SQLite relational database to store data. Among the features provided are proﬁle and login, an image drawing tool, wiki-like pages of all entries and a search tool. We would like to emphasize here that there is no need to register or to log in to view the content of the database. However, the proﬁle and login features have been provided for collaborators and ‘super users’ who are inter- ested not only in viewing, but also editing the content of the database. Creating an account and loging into the database give the user access to the admin site of the database, but also uncovers the wiki-like pages of the entries. By entering the administration site it is possible to add new data, delete information, edit and correct mistakes. Editing information about proteins, genes, diseases and types of damage is also available via wiki-like pages, from the pages of particular database entries. Users can also add comments and new references to existing records. The image drawing tool (accessible via a ‘draw a picture’ link in the main menu) system has been de- veloped to illustrate all steps of DNA repair pathways Nucleic Acids Research, 2011, Vol. 39, Database issue D791 as protein–DNA complexes, in which proteins are dis- played in the textbook-like format of ‘potato models’ (ellipsoids). However, it can be also used as a standalone tool (without any connection to REPAIRtoire) to create images of protein–protein or protein–DNA complexes. The drawing engine uses the SVG format provided by the W3C consortium, and enables exporting the image in the JPEG format. The SVG format enables resizing the images without the loss of the quality and makes it possible to modify them with external tools for vector graphics processing, e.g. Inkscape or others free or com- mercially available software. The REPAIRtoire database can be queried using a simple text search tool, available in the main menu. The tool returns a structured list of entries in the database that contain the query (e.g. ‘cancer’, ‘DNA polymerase’, ‘crosslink’, ‘adenine’, etc. or a name of the author). In future, we plan to introduce ﬁltering and advanced search options (e.g. to enable sorting according to the relevance to the query). DISCUSSION The topic of DNA repair is covered by many computa- tional resources; however, thus far there has been no specialized database dedicated to DNA repair pathways. The repairGENES database (http://www.repairgenes.org/) collects information about genes encoding proteins involved in DNA repair and connects information taken from sequence and ontology databases. Repair-FunMap (24) used to provide information about the network of interactions between proteins involved in DNA re- pair and other proteins, but to our best knowledge it is no longer available. Information about DNA repair pathways and their components is available also in general-purpose pathway databases such as KEGG (25) or REACTOME (26). REPAIRtoire is dedicated to DNA repair and it contains more detailed and select information than the general-purpose pathway databases. An import- ant component of REPAIRtoire that to our knowledge is not present in other databases is the dataset of DNA damage, connected to potential causes of each lesion as well as to effects if they are not removed. REPAIRtoire is also unique in that it provides reciprocal links between the damage (or its more general type) and the proteins that can detect and remove it. Our literature survey has also revealed a greater number of connections between particu- lar DNA lesions and the respective proteins that can detect and remove it than can be found in general databases. In the development of REPAIRtoire, we used our ex- perience from the work on the MODOMICS database of RNA modiﬁcation pathways (27,28). We hope that this database will become comparably popular and useful for the community of researchers working on DNA repair, as MODOMICS has become in the RNA modiﬁcation com- munity. In the future, we plan to integrate these databases using a common data model and a joint interface, and to extend the database system to cover the entire metabolism of nucleic acids.