Applied Bioinformatics Course

List of databases

• NAR databases - The most extensive list of biological databases being maintained by the international journal Nuclei Acids Research which publishes a special issue for molecular biology databases in the first issue of each year since 1996. All these database papers can be accessed freely. You may find links to the web site of the databases described in the paper.
• NCBI databases - The molecular databases maintained by NCBI. A Flash flowchart for 24 databases connected by lines shows the relationships and internal links among all these databases. These databases are divided into 6 major groups: nucleotide, protein, structure, taxonomy, genome and expression. It also provides links to the individual database description page.
• EBI databases - The main portal to all EBI databases divided in several groups, such as literature, microarray, nucleotide, protein, structure, pathway, ontology, etc. Links to database query and retrieve systems can be found in this portal.

Database query systems

• NCBI Entrez - The unique interface to search all NCBI databases. Query results are displayed with entry numbers along the database names.
• EBI SRS - The database query system maintained by EBI. SRS stands for sequence retrieval system which was originally developed by Thure Etzold at the European Molecular Biology Laboratory in early 1990' and moved to EBI. It was originally an open system and installed in dozen of institutions with different databases. In late 1990', SRS became a commercial package but still free to academic. In 2006, SRS was acquired by BioWisdom, a software company based in Cambridge, UK.
• EMBL SRS - The database query system (ver 8.2) maintained by EMBL, at Germany.
• DKFZ SRS - The database query system (ver 8.2) maintained by German Cancer Research Center.
• Columbia SRS - The database query system (ver 8.2) maintained by Columbia University, US.
• CMBI MRS - The open source database query system developed by Marteen Hekkelman at the Center for Molecular and Biomolecular Information (CMBI), the Netherlands.
• CBI MRS - The MRS installed at the Center for Bioinformatics, Peking University.