Development of the Overlapping Oligonucleotide Database and its application to signal sequence search of the human...

We have developed ODS (Overlapping Oligonucleotide Database for Signal Sequence Search)--the first relational database that integrates information on biological features into the search for signal sequences. In existing biological sequence databases, even relational ones, retrieving nucleotide sequences based on their biological features involves much labour and time or even the development of a new program. GenBank sequence data, including FEATURES records, are organized into three relational tables in ODS. Nucleotide sequences are transformed into overlapping oligonucleotides in order to facilitate the signal sequence search rapidly without the need for specific alignment programs. This transformation leads to a one-to-one correspondence between the nucleotide sequence and its biological feature. The signal sequence search by ODS is done in SQL queries and ODS obviates the need for molecular biologists to write computer programs. The application of ODS to searches of promoter regions revealed putative cis-acting elements and basic statistical analyses of occurrences of oligonucleotides showed interesting findings concerning the 'cg' dinucleotide.