We have recently found that the computation time of homology-based subcellular localization can be substantially reduced by aligning profiles up to the cleavage site positions of s...
Abstract. Local similarity is an important tool in comparative analysis of biological sequences, and is therefore well studied. In particular, the Smith-Waterman technique and its ...
Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren...
The task of aligning sequences arises in many applications. Classical dynamic programming approaches require the explicit state enumeration in the reward model. This is often impr...
Andreas Karwath, Kristian Kersting, Niels Landwehr
With the advent of XML we have seen a renewed interest in methods for computing the difference between trees. Methods that include heuristic elements play an important role in pr...
Tancred Lindholm, Jaakko Kangasharju, Sasu Tarkoma
We describe a novel hardware architecture for genomic and proteomic sequence alignment which achieves a speed-up of two to three orders of magnitude over Smith-Waterman dynamic pr...