Alberto Riva



Title: Implementation and Usage of the CL-DNA Library


Abstract Our group at the Children's Hospital Informatics Program (CHIP) is using Common Lisp to develop innovative, interoperable, web-based bioinformatics applications. Our main focus is on the integration of data from different sources and online resources, leading to applications that effectively help researchers mine and analyze biomedical data. We have found Common Lisp to be an excellent platform for the development of bioinformatics applications, thanks to its ability for rapid prototyping, the powerful and flexible data structures it offers, and its dynamic nature. In this talk we describe CL-DNA, a library of Common Lisp code that we developed to handle and manipulate genetic data, and that lies at the core of our applications. Our library provides data structures and functions to efficiently represent DNA and amino acid sequences, to describe mutations, to perform sequence translation, search and matching, to analyze sequences, to access online genetic resources. We will describe the design and implementation of the library, and discuss its usage through examples taken from actual running systems