Sequence Comparison Using a Relational Database Approach

A variety of heterogenous data sources is available in the field of molecular biology. Our focus lies on the biological sequence data, i. e. data maintained in collections like EMBL or SWISS-PROT. We propose a relational model based on an Entity-Relationship approach for this discourse world. This is the foundation of a flexible architecture useful for a variety of purposes, e. g. for sequence comparison. In this paper we present our first application system within this architecture, the sequence analysis tool NNSAT. The description of this system is accompanied by a short review of the data model and a section on the problem of sequence comparison in which we propose a small modification of the Needleman and Wunsch alignment method.