PALINGOL - A DECLARATIVE PROGRAMMING LANGUAGE TO DESCRIBE NUCLEIC-ACIDS SECONDARY STRUCTURES AND TO SEQUENCE DATABASES

At the RNA/RNA level, biological signals are defined by a combination of spatial structures and sequence motifs. Until now, few attempts had been made in writing general purpose search programs that take into a ccount both sequence and structure criteria. Indeed, the most successf ul structure scanning programs are usually dedicated to particular str uctures and are written using general purpose programming languages th rough a complex and time consuming process where the biological proble m of defining the structure and the computer engineering problem of lo oking for it are intimately intertwined. In this paper, we describe a general representation of structures, suitable for database scanning, together with a programming language, Palingol, designed to manipulate it. Palingol has specific data types, corresponding to structural ele ments-basically helices-that can be arranged in any way to form a comp lex structure. As a consequence of the declarative approach used in Pa lingol, the user should only focus ion 'what to search for' while the language engine takes care of 'how to look for it'. Therefore, it beco mes simpler to write a scanning grogram and the structural constraints that define the required structure are more clearly identified.