Alberto Riva |
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Title: Implementation and Usage of the CL-DNA Library |
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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
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