A Constraint Based Structure Description Language for Biosequences

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. Keywords: constraints, biostructures, description language, searching. 1 Introduction The aim of the work described in this paper is to use constraint solving techniques to search for structural patterns in sequences (or st..

A Constraint Based Structure Description Language for Biosequences

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 the 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 ideas for an implementation of the CSP structure searching algorithm in C++. Keywords: constraints, biostructures, description language, searching. Contents 1 Introduction 3 2 Biological motivation 5 2.1 Example structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 3 Previous approaches 8 3.1 General pu..

StructWeb: Biosequence structure searching on the Web using clp(FD)

We describe an implementation in a finite domain constraint logic programming language of a web-based biosequence structure search program. We have used the clp(FD) language for the implementation of our search engine and have ported the PiLLoW libraries to clp(FD). Our program is based on CBSDL, a constraint based structure description language for biosequences, and uses constrained descriptions to search for the structures in biosequences, such as tandem repeats, stem loops, palindromes and pseudo-knots. We also discuss issues encountered in porting the PiLLoW libraries to clp(FD) and the design and construction of the Web interface that we have constructed for our search engine. Keywords: constraints, biostructures, description language, searching, WWW interface. 1 Introduction In this paper we report an implementation of a web-based biosequence structure searching program. This implementation has been constructed using the finite domain constraint logic programming language clp(FD..