32

Non-Invasive Diagnostic Tools. Genes (Basel) 2016 Dec 26;8(1). pii: E8. https://

doi.org/10.3390/genes8010008).

(b) Become familiar with different target prediction algorithms and their different

parameters (e.g., TargetScan, miRanda, and PITA).

Useful Tools and Web Links

Rfam

https://rfam.xfam.org/

RNAAnalyzer

https://rnaanalyzer.bioapps.biozentrum.uni-­wuerzburg.de/

mFold web server

https://unafold.rna.albany.edu/?q=mfold (out of service since November

1, 2020)

RNAfold web

server

https://rna.tbi.univie.ac.at/cgi-­bin/RNAWebSuite/RNAfold.cgi (replaces

mfold since 1.11.20)

ViennaRNA

Package

https://www.tbi.univie.ac.at/RNA/

Freiburg RNA

Tools

https://rna.informatik.uni-­freiburg.de/

regRNA

https://regrna2.mbc.nctu.edu.tw/

Riboswitch Finder

https://riboswitch.bioapps.biozentrum.uni-­wuerzburg.de/

Dandekar and Bengert (2002) RNA Motifs and Regulatory Elements. Springer Verlag, 2002

(https://books.google.de/books?id=hOLtCAAAQBAJ&hl=de)

Dandekar and Sharma (1998) Regulatory RNA. Springer Verlag, 1998 (https://books.google.

de/books?id=j7LoCAAAQBAJ&hl=de)

(c) Look for miRNAs that indicate a possible interaction with Brca1 (e.g. https://www.

microrna.org and https://www.targetscan.org – do miRNAs find each other?).

Literature

Bengert P, Dandekar T (2003) A software tool-box for analysis of regulatory RNA elements. Nucl

Acids Res 31:3441–3445

Chang TH, Huang HY, Hsu JB et al (2013) An enhanced computational platform for investigating the

roles of regulatory RNA and for identifying functional RNA motifs. BMC Bioinformatics 14(2):4

Dandekar T, Bengert P (2002) RNA motifs and regulatory elements. Springer. https://books.google.

de/books?id=hOLtCAAAQBAJ&hl=de

Dandekar T, Sharma K (1998) Regulatory RNA. Springer. https://books.google.de/books?id=j7Lo

CAAAQBAJ&hl=de

Eddy SR (2004) How do RNA folding algorithms work? Nat Biotechnol 22:1457–1458

Gardner PP, Daub J, Tate J et al (2011) Rfam: Wikipedia, clans and the “decimal” release. Nucleic

Acids Res 39(Database issue):D141–D145. https://doi.org/10.1093/nar/gkq1129

2  Magic RNA