A Constraint Based Structure Description Language for Biosequences
- Cite this article as:
- Eidhammer, I., Jonassen, I., Grindhaug, S.H. et al. Constraints (2001) 6: 173. doi:10.1023/A:1011481521835
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We report an investigation into how constraint solving techniques can be used to search for patterns in sequences (or strings) of symbols over a finite alphabet. We define a constraint-based structure description language for biosequences, and give the definition of an algorithm to solve the structure searching problem as a CSP. The methodology which we have developed is able to describe two-dimensional structure of biosequences, such as tandem repeats, stem loops, palindromes and pseudo-knots. We also report on an implementation of the language in the constraint logic programming language clp(FD), with test results of a simple searching algorithm, and results from a preliminary implementation in C++ using consistency checking techniques from solving CSP.