A MEMORY EFFICIENT ALGORITHM FOR STRUCTURAL ALIGNMENT OF RNAs WITH EMBEDDED SIMPLE PSEUDOKNOTS

Abstract

In this paper, we consider the problem of structural alignment of a target RNA sequence of length n and a query RNA sequence of length m with known secondary structure that may contain embedded simple pseduoknots. The best known algorithm for solving this problem (Dost et al. [13]) runs in O(mn4) time with space complexity of O(mn3), which requires too much memory making it infeasible for comparing ncRNAs (non-coding RNAs) with length several hundreds or more. We propose a memory efficient algorithm to solve the same problem. We reduce the space complexity to O(mn2 + n3) while maintaining the same time complexity of Dost et al.'s algorithm. Experimental reslts show that our algorithm is feasible for comparing ncRNAs of length more than 500. Availability: The source code of our program is available upon request.

Anxiety and Osteoarthritis Disability: Updated Overview and Commentary

“…While generally poorly studied at the early disease stages, it appears that as the disease progresses and requires surgical intervention, almost 50 percent of preoperative osteoarthritis surgical cases may be expected to exhibit anxiety symptoms as observed by Jones et al [19]. While this high number of anxious cases may have been attributable in part to the selfreport mode of estimating anxiety as normal or abnormal, Wong et al [20] as well as Castano et al [21], Stubbs et al [5] and Guglielmo et al [22] all reported the presence of anxiety to be of the order of 20 percent or higher in various osteoarthritis or arthritis samples when this has been assessed.…”

A novel two-level particle swarm optimization approach to train the transformational grammar based hidden Markov models for performing structural alignment of pseudoknotted RNA

“…RNA structural alignment, also known as RNA sequence-structure alignment, is the challenging area of bioinformatics, which becomes more challenging and advantageous if the pseudoknots are also considered in the structure. The literature available on pseudoknotted structural alignment of RNA includes simulated annealing [1]; dynamic programming [2][3][4][5][6][7][8][9][10][11][12][13][14][15][16]; genetic algorithm [17][18][19]; integer linear programming [20][21][22][23]; graph approach [24][25][26][27]; tree construction [28][29][30][31]; stochastic sampling [32]; Markov chain Monte Carlo [33] and formal grammar [34][35][36].…”