Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams
نویسندگان
چکیده
منابع مشابه
Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams
MOTIVATION The secondary structure of RNA is integral to the variety of functions it carries out in the cell and its depiction allows researchers to develop hypotheses about which nucleotides and base pairs are functionally relevant. Current approaches to visualizing secondary structure provide an adequate platform for the conversion of static text-based representations to 2D images, but are li...
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Pseudoknots are widely occurring structural motifs in RNA. Pseudoknots have been shown to be functionally important in different RNAs which play regulatory, catalytic, or structural roles in cells. Current biophysical methods to identify the presence of pseudoknots are extremely time consuming and expensive. Therefore, bioinformatics approaches to accurately predict such structures are highly d...
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SUMMARY There are many programs that can read the secondary structure of an RNA molecule and draw a diagram, but hardly any that can cope with 10(3) bases. RNAfdl is slow but capable of producing intersection-free diagrams for ribosome-sized structures, has a graphical user interface for adjustments and produces output in common formats. AVAILABILITY AND IMPLEMENTATION Source code is availabl...
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Recent advances in RNA structure determination include using data from high-throughput probing experiments to improve thermodynamic prediction accuracy. We evaluate the extent and nature of improvements in data-directed predictions for a diverse set of 16S/18S ribosomal sequences using a stochastic model of experimental SHAPE data. The average accuracy for 1000 data-directed predictions always ...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2015
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btv372