Nucleic Acids Research, Vol 24, Issue 8 1395-1403, Copyright © 1996 by Oxford University Press
B Billoud, M Kontic and A Viari
At the DNA/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 account both
sequence and structure criteria. Indeed, the most successful structure
scanning programs are usually dedicated to particular structures and are
written using general purpose programming languages through a complex and
time consuming process where the biological problem of defining the
structure and the computer engineering problem of looking 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 elements-basically helices-that can be
arranged in any way to form a complex structure. As a consequence of the
declarative approach used in Palingol, the user should only focus on 'what
to search for' while the language engine takes care of 'how to look for
it'. Therefore, it becomes simpler to write a scanning program and the
structural constraints that define the required structure are more clearly
identified.
ARTICLES
Palingol: a declarative programming language to describe nucleic acids' secondary structures and to scan sequence database
Atelier de Bio-informatique URA CNRS 448, Institut Curie, Paris, France.
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