Structurome

About Structurome Module

The Structurome module provides RNA secondary structure predicted by different algorithms while enhanced with/without secondary structure profiling data at RBP binding sites. Binding sites are extended to at least 150nt and both the reactivity from experiments and the secondary structure model are provided.



References:
1. PARS: Kertesz M, Wan Y, Mazor E, et al. Genome-wide measurement of RNA secondary structure in yeast. Nature. 2010;467(7311):103-107.
2. DMS-seq: Rouskin S, Zubradt M, Washietl S, Kellis M, Weissman JS. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature. 2014;505(7485):701-705.
3. CIRS-seq: Incarnato D, Neri F, Anselmi F, Oliviero S. Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome. Genome Biol. 2014;15(10):491.
4. ChemModeSeq: Hector RD, Burlacu E, Aitken S, et al. Snapshots of pre-rRNA structural flexibility reveal eukaryotic 40S assembly dynamics at nucleotide resolution. Nucleic Acids Res. 2014;42(19):12138-12154.
5. DMS-MaPseq: Zubradt M, Gupta P, Persad S, Lambowitz AM, Weissman JS, Rouskin S. DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo. Nat Methods. 2017;14(1):75-82.
6. icSHAPE: Spitale RC, Flynn RA, Zhang QC, et al. Structural imprints in vivo decode RNA regulatory mechanisms. Nature. 2015;519(7544):486-490.
7. ENCODE icSHAPE: ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57-74.
8. RNAstructure (Fold): Reuter JS, Mathews DH. RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics. 2010;11:129.
9. ViennaRNA (RNAfold): Lorenz R, Bernhart SH, Höner Zu Siederdissen C, et al. ViennaRNA Package 2.0. Algorithms Mol Biol. 2011;6:26.
10. Structure Surfer: Berkowitz ND, Silverman IM, Childress DM, Kazan H, Wang LS, Gregory BD. A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer). BMC Bioinformatics. 2016;17(1):215.
11. RNAex: Wu Y, Qu R, Huang Y, et al. RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data. Nucleic Acids Res. 2016;44(W1):W294-W301.
12. Forna: Kerpedjiev P, Hammer S, Hofacker IL. Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams. Bioinformatics. 2015;31(20):3377-3379.