No abstract

Abstract-Sorting by reversals is an important problem in inferring the evolutionary relationship between two genomes. The problem of sorting unsigned permutation has been proven to be NP-hard. The best guaranteed error bounded is the 3/2-approximation algorithm. However, the problem of sorting signed permutation can be solved easily. Fast algorithms have been developed both for finding the sorting sequence and finding the reversal distance of signed permutation. In this paper, we present a way to view the problem of sorting unsigned permutation as signed permutation. And the problem can then be seen as searching an optimal signed permutation in all n 2 corresponding signed permutations. We use genetic algorithm to conduct the search. Our experimental result shows that the proposed method outperform the 3/2-approximation algorithm.

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No abstract

Correct alignment of protein sequences is critical for accurate understanding of the evolution of the protein. Therefore, it is important to know how likely an alignment is correct. Any approach that uses randomized sequences to access significance uses only part of the information inherent in an amino acid sequence. Offset alignment evaluation is a method to model and estimate the confidence of a given protein sequence alignment, which takes into account the inherent information from the protein sequence secondary structures. The confidence of a given alignment is estimated by a significance score based on the set of offset alignments. Finally, we introduce OAE, a Java implementation of the Offset alignment evaluation which is freely available to the public.

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No abstract