SeqFold: Genome-scale reconstruction of RNA secondary structure integrating experimental measurements

Reference | Instructions | Downloads | Sample output | License | Contact |



SeqFold is a tool for RNA secondary structure prediction from experimental data. Given high-throughput data, it can reconstruct the secondary structures of the whole transcriptome, termed the RNA structurome. It outputs reconstructed RNA secondary structure as well as base-level accessibilities for each transcript. Input data types include parallel analysis of RNA structure (PARS), selective 2’-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq), fragmentation sequencing (FragSeq), and conventional SHAPE data.

Reference

Ouyang Z, Snyder MP, and Chang HY (2012) SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data. Genome Research. [web]

Instructions

How to prepare the data
How to run SeqFold
How to interpret the results


Downloads

Source code
Sample data

Sample output

The secondary structure of noncoding RNA SNR10


License

Use of SeqFold is free for non-commercial research. Commercial users please contact the authors.

Contact

Zhengqing Ouyang: zhengqing.ouyang AT jax.org