Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix
نویسندگان
چکیده
منابع مشابه
Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix
It has become clear that noncoding RNAs (ncRNA) play important roles in cells, and emerging studies indicate that there might be a large number of unknown ncRNAs in mammalian genomes. There exist computational methods that can be used to search for ncRNAs by comparing sequences from different genomes. One main problem with these methods is their computational complexity, and heuristics are ther...
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MOTIVATION Structural alignment methods are widely used to generate gold standard alignments for improving multiple sequence alignments and transferring functional annotations, as well as for assigning structural distances between proteins. However, the correctness of the alignments generated by these methods is difficult to assess objectively since little is known about the exact evolutionary ...
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MOTIVATION The level of sequence conservation between related nucleic acids or proteins often varies considerably along the sequence. Both regions with high variability (mutational hot-spots) and regions of almost perfect sequence identity may occur in the same pair of molecules. The reliability of an alignment therefore strongly depends on the level of local sequence similarity. Especially in ...
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MOTIVATION Multiple structural alignments (MSTAs) provide position-specific information on the sequence variability allowed by protein folds. This information can be exploited to better understand the evolution of proteins and the physical chemistry of polypeptide folding. Most MSTA methods rely on a pre-computed library of pairwise alignments. This library will in general contain conflicting r...
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ژورنال
عنوان ژورنال: PLoS Computational Biology
سال: 2007
ISSN: 1553-7358
DOI: 10.1371/journal.pcbi.0030193