A RAPID ACCESS MOTIF DATABASE (RAMDB) WITH A SEARCH ALGORITHM FOR THERETRIEVAL PATTERNS IN NUCLEIC-ACIDS OR PROTEIN DATA-BANKS

We present here a codification structure, entirely interfaced with the main packages for biomolecule database management, associated with a new search algorithm to retrieve quickly a sequence in a database. Thi s sq stem is derived from a method previously proposed for homology se arch in databanks with a preprocessed codification of an entire databa se in which all the overlapping subsequences of a specific length in a sequence were converted into a code and stored in a hash-coding file. This new algorithm is designed far an improved use of the codificatio n. It is based on the recognition of the rarest strings which characte rize the query sequence and the inter section of sorted lists read in the codification structure. The system is applicable to both nucleic a cid and protein sequences and is used to find patterns in databanks or large sets of sequences. A few examples of applications are given. In addition, the comparison of our method with existing ones shows that this new approach speeds up the search for query patterns in large dat a sets.