PairsDB protein alignment atlas – Interface and database tables

Kimmo Mattila


On EMBnet news vol13 Nr 4 (2007) we presented the PairsDB protein sequence alignment database that contains directly computed or hierarchically inferred pairwise alignments for all known protein sequences. Since 2007 several small modifications have been made to the database and the WWW interface (http.// The database itself has been updated twice. The latest release (1/2009) is based on the protein sequences collected from protein databases in February 2009.


In this article we provide an updated description about the interface and also discuss the general features of the most essential SQL database tables of PairsDB. The data collected to the PairsDB database is freely available and provides a unique resource for studying the currently known protein universe with the methods of bioinformatics and data mining.


Protein; Alignment; BLAST; Database


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