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Old 07-14-2017, 06:53 AM   #1
Eurioste
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Question Good RNA folding tools

Does anybody knows a good tool for predicting RNA secondary structure of 160,074 RNA sequences (most about 300 bps long), other than Vienna RNAfold? Even better if the tools is available in a web-server that can support batch queries.
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Old 07-14-2017, 02:52 PM   #2
fanli
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RNAstructure is another alternative:
http://rna.urmc.rochester.edu/RNAstructure.html

CentroidFold is another:
https://github.com/satoken/centroid-rna-package

If you have that many sequences, you're better off downloading the command-line versions and running the jobs on a cluster.
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Old 07-16-2017, 01:31 AM   #3
ppgardne
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Single sequence structure prediction is extremely unreliable (https://bmcbioinformatics.biomedcent...471-2105-5-140). You're better of building alignments and folding those with e.g. RNAalifold. R-scape will tell you if you there is significant covariation.

I hear CONTRAfold is reasonably accurate, if you must fold single sequences.
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