SimSearch: A New Variant of Dynamic Programming Based on Distance Series for Optimal and Near-Optimal
Similarity Discovery in Biological Sequences

Sérgio A.D. Deusdado1, Paulo M.M. Carvalho2

Escola Superior Agrária1
Instituto Politécnico de Bragança
P-5300 Bragança, Portugal

<>Universidade do Minho2
Departamento de Informática
P-4710-057 Braga, Portugal

E-mail: pmc at


In this paper, we propose SimSearch, an algorithm implementing a new variant of dynamic programming based on distance series for optimal and near-optimal similarity discovery in biological sequences. The initial phase of SimSearch is devoted to fulfil the binary similarity matrices by signalling the distances between occurrences of the same symbol. The scoring scheme is further applied, when analysed the maximal extension of the pattern. Employing bit parallelism to analyse the global similarity matrix’s upper triangle, the new methodology searches the sequence(s) for all the exact and approximate patterns in regular or reverse order. The algorithm accepts parameterization to work with greater seeds for near-optimal results. Performance tests show significant efficiency improvement over traditional optimal methods based on dynamic programming. Comparing the new algorithm’s efficiency against heuristic based methods, equalizing the required sensitivity, the proposed algorithm remains acceptable.
IWPACBB'08, Salamanca, Spain, October 2008