Showing papers by "Abbas Nowzari-Dalini published in 2010"
TL;DR: A heuristic method based on genetic algorithm to find reasonable solution within acceptable time for single Nucleotide Polymorphisms and results show that this method can obtain optimal solutions in almost all cases and runs much faster than exact algorithm when the number of SNP sites is large.
27 citations
TL;DR: A new efficient algorithm is presented for haplotype block partitioning based on haplotype diversity that can be performed in polynomial time complexity with regard to the number of haplotypes and SNPs.
9 citations
TL;DR: A new algorithm for generating the possible shapes of a single-stranded RNA molecule of length ℓ is presented, using a bijection between the secondary structure and specific ordered trees to generate different types of RNA.
Abstract: The structure of RNA is often the key to its function and there is a close relationship between structure and function in biology. In this paper, we present a new algorithm for generating the possible shapes of a single-stranded RNA molecule of length l. We use a bijection between the secondary structure and specific ordered trees. Hence, generating different types of RNA becomes equivalent to the generation of these trees. The generated trees are encoded as integer sequences and are produced in A-order. The time complexity of the presented algorithm is O(l-k) where l is the number of bases and k, the number of pairings. Ranking and unranking algorithms with O(kl-k2) and O(l2+k2) time complexity are also presented.
9 citations