Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Could anyone suggest me good whole genome alignment tools? abysslover Bioinformatics 7 01-03-2017 07:16 AM
Is there any good statistic way or tools to compare the read count owwa Bioinformatics 7 04-20-2014 04:21 PM
Good poly-A filtering rules or tools ysnapus Bioinformatics 0 07-03-2013 11:59 AM
Could I make any RNA folding pages shown with pre-filled sequence in URL? vixensjlin Bioinformatics 3 04-30-2013 10:11 PM
Folding RNA (urgent) renesh Bioinformatics 1 01-16-2013 03:07 PM

Thread Tools
Old 07-14-2017, 07:53 AM   #1
Junior Member
Location: Brazil

Join Date: Jun 2017
Posts: 5
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.
Eurioste is offline   Reply With Quote
Old 07-14-2017, 03:52 PM   #2
Senior Member
Location: California

Join Date: Jul 2014
Posts: 198

RNAstructure is another alternative:

CentroidFold is another:

If you have that many sequences, you're better off downloading the command-line versions and running the jobs on a cluster.
fanli is offline   Reply With Quote
Old 07-16-2017, 02:31 AM   #3
Location: New Zealand

Join Date: Oct 2010
Posts: 13

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.
ppgardne is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 05:58 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO