31

1. Can a potential IRE motif be found?

2. Now

use

the

RNAAnalyzer

(https://rnaanalyzer.bioapps.biozentrum.uni-­

wuerzburg.de/) for this examination.

Which of the following statements is correct (multiple answers possible)?

(A) The exercise example is an IRE.

(B) Besides the IRE, the RNAAnalyzer does not find any other elements for the exer­

cise example, e.g. no “Catalytic RNA”.

(C) The RNAAnalyzer finds an IRE at position 71 for the exercise example.

(D) One IRE is the consensus sequence “CAGUGN”, the RNAAnalyzer also found

this in the exercise example.

Task 2.7

Example: Perform a search with the Riboswitch Finder (https://riboswitch.bioapps.biozen­

trum.uni-­wuerzburg.de/) using the following sequence (please just use the sequence exam­

ple from the Riboswitch Finder page): Streptococcus pyogenes STPY1 (https://riboswitch.

bioapps.biozentrum.uni-­wuerzburg.de/examples.html).

Which of the following statements is correct (multiple answers possible)?

(A) The Riboswitch Finder finds three possible hits for a riboswitch for the example

sequence, they are all on the minus strand.

(B) All hits found for the example sequence are of poor quality (sequence, structure,

energy), thus indicating no possible riboswitches.

(C) The Riboswitch Finder finds three possible riboswitches on the plus strand at

position 1288 for the example sequence.

(D) The hits found for the example sequence have, among others, three stem-loops in

their secondary structure.

(E) Riboswitches are the only regulatory RNA elements in prokaryotes.

Task 2.8

Example: Analyze the 18 S-rRNA gene from Cordulegaster boltonii (GenBank ID:

FN356072.1) for a possible ITS2 secondary structure using the ITS2 database (https://its2.

bioapps.biozentrum.uni-­wuerzburg.de/).

Task 2.9

Example:

(a) Familiarize yourself with non-coding RNAs (e.g. miRNAs and lncRNAs). Use e.g.

https://www.microrna.org, https://www.mirbase.org, https://lncipedia.org/ and

https://www.targetscan.org, but also our two articles (Kunz M et al. Bioinformatics

of cardiovascular miRNA biology. J Mol Cell Cardiol 2015 Dec;89(Pt A):3–10.

https://doi.org/10.1016/j.yjmcc.2014.11.027; Kunz M et al. Non-Coding RNAs in

Lung Cancer: Contribution of Bioinformatics Analysis to the Development of

2.3  Exercises for Chap. 2