In this paper we describe a new DNA compression algorithm. It is well known that one of the main features of DNA sequences is that they contain substrings which are duplicated except for a few random mutations. For this reason most DNA compressors work by searching and encoding approximate repeats. We depart from this strategy by searching and encoding only exact repeats. However, we use an enc...

DNA computing has been applied to many different decision or combinatorial problems when being proved of its feasibility in experimental demonstration. In this paper, for the objective to reduce the DNA volume of the dominating set problem which belongs to the NPcomplete problem, the pruning strategy is introduced into the DNA supercomputing and a new DNA algorithm is advanced. The new algorith...

We present an algorithm that solves the Minimal Set Cover prob lem within the framework of a surface based model of computation A xing DNA strands to a solid surface reduces the possibility of error resulting from the loss of DNA strands in solution An algorithm solving the Minimal Set Cover problem has previously been proposed using the sticker model of DNA computation Roweis We show that by t...

We discuss a model for the evolutionary distance between two coding DNA sequences which specializes to the DNA/protein model proposed in Hein [3]. We discuss the DNA/protein model in details and present a quadratic time algorithm that computes an optimal alignment of two coding DNA sequences in the model under the assumption of affine gap cost. The algorithm solves a conjecture in [3] and we be...

The DNA fragment assembly is an essential step in DNA sequencing projects. Since DNA sequencers output fragments, the original genome must be reconstructed from these small reads. In this paper, a new fragment assembly algorithm, Pattern Matching based String Graph Assembler (PMSGA), is presented. The algorithm uses multipattern matching to detect overlaps and a minimum cost flow algorithm to d...