RNA structure and structural alignment
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Relation Between RNA Sequences, Structures, and Shapes via Variation Networks
Background: RNA plays key role in many aspects of biological processes and its tertiary structure is critical for its biological function. RNA secondary structure represents various significant portions of RNA tertiary structure. Since the biological function of RNA is concluded indirectly from its primary structure, it would be important to analyze the relations between the RNA sequences and t...
متن کاملLocal RNA structure alignment with incomplete sequence
MOTIVATION Accuracy of automated structural RNA alignment is improved by using models that consider not only primary sequence but also secondary structure information. However, current RNA structural alignment approaches tend to perform poorly on incomplete sequence fragments, such as single reads from metagenomic environmental surveys, because nucleotides that are expected to be base paired ar...
متن کاملPrediction of Pseudoknotted RNA Structure by a Structural Alignment Using GeneticAlgorithm
Developing an efficient algorithm for predicting a pseudoknot structure of RNA has been a challenging problem because of its high computational complexity in both time and space. Structural alignment is one of the RNA secondary structure prediction methods, which predicts a secondary structure by aligning an RNA (called slave sequence) whose structure is unknown to an RNA (master sequence) with...
متن کاملDAFS: simultaneous aligning and folding of RNA sequences via dual decomposition
MOTIVATION It is well known that the accuracy of RNA secondary structure prediction from a single sequence is limited, and thus a comparative approach that predicts a common secondary structure from aligned sequences is a better choice if homologous sequences with reliable alignments are available. However, correct secondary structure information is needed to produce reliable alignments of RNA ...
متن کاملRNA Structural Alignment with Conditional Random Fields
Computationally identifying non-coding RNA regions on the genome has much attention to be investigated. However, it is essentially harder than gene-finding problems for protein-coding regions because non-coding RNA sequences do not have a strong statistical signals. Since comparative sequence analysis is effective for non-coding RNA detection, efficient computational methods are expected for st...
متن کاملStructural Local Multiple Alignment of RNA
Today, RNA is well known to perform important regulatory and catalytic function due to its distinguished structure. Consequently, state-of-the-art RNA multiple alignment algorithms consider structure as well as sequence information. However, existing tools neglect the important aspect of locality. Notably, locality in RNA occurs as similarity of subsequences as well as similarity of only substr...
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تاریخ انتشار 2010