Efficient Alignment of RNAs with Pseudoknots Using Sequence Alignment Constraints
نویسندگان
چکیده
منابع مشابه
Efficient Alignment of RNAs with Pseudoknots Using Sequence Alignment Constraints
When aligning RNAs, it is important to consider both the secondary structure similarity and primary sequence similarity to find an accurate alignment. However, algorithms that can handle RNA secondary structures typically have high computational complexity that limits their utility. For this reason, there have been a number of attempts to find useful alignment constraints that can reduce the co...
متن کاملStructural Alignment of RNAs with Pseudoknots
Non-coding RNAs (ncRNAs) are found to be critical for many biological processes. However, identifying these molecules is very difficult and challenging due to the lack of strong detectable signals such as opening read frames. Most computational approaches rely on the observation that the secondary structures of ncRNA molecules are conserved within the same family. Aligning a known ncRNA to a ta...
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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 compa...
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Given two sequences S1, S2 and a constrained sequence C, the longest common subsequence of S1, S2 with restriction to C is defined as the constrained longest common subsequence (CLCS) of S1, S2 and C. At the same time, the best alignment of S1, S2 with restriction to C is defined as the constrained pairwise sequence alignment (CPSA) of S1, S2 and C. Previous algorithms have shown that both CLCS...
متن کاملA memory-efficient algorithm for multiple sequence alignment with constraints
MOTIVATION Recently, the concept of the constrained sequence alignment was proposed to incorporate the knowledge of biologists about structures/functionalities/consensuses of their datasets into sequence alignment such that the user-specified residues/nucleotides are aligned together in the computed alignment. The currently developed programs use the so-called progressive approach to efficientl...
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ژورنال
عنوان ژورنال: EURASIP Journal on Bioinformatics and Systems Biology
سال: 2009
ISSN: 1687-4145,1687-4153
DOI: 10.1155/2009/491074