Efficient Sequence Alignment with Side-Constraints by Cluster Tree Elimination
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...
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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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Cluster and mini-cluster tree elimination are well-known solving methods for constrained optimization problems, developed for the centralized case. These methods, based on cost function combination, can be easily reformulated as synchronous algorithms to solve the distributed versions of the above mentioned problems. During solving they exchange a linear number of messages, but these messages c...
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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...
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In many situations, automated multi-alignment programs are not able to correctly align families of nucleic acid or protein sequences. Difficult cases comprise not only distantly related sequences but also tandem duplications independent of their evolutionary age. Frequently, additional biological information is available that establishes homologies at least in parts of the sequences based on st...
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ژورنال
عنوان ژورنال: Constraints
سال: 2008
ISSN: 1383-7133,1572-9354
DOI: 10.1007/s10601-007-9032-x