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(general STOP signal) and the ppGpp (messenger). For the example sequence, the

­riboswitch finder should have found three possible riboswitches on the plus strand at posi­

tion 1288, which have three stem-loops in their secondary structure. These three different

hits come from different folding possibilities of the secondary structure, where in this case

two show a good quality of folding energy, i.e. have a more stable structure.

20.4

Example 2.8

You should find the typical four helices of an ITS2 secondary structure (you can also

use RNAfold to fold the secondary structure to check).

(Example sequence can be found here: https://www.ncbi.nlm.nih.gov/nuccor

e/260206998?report=fasta; simply copy it into the search window of the ITS2 database

and use the default parameters).

Example 2.9

(a) For this, look at the recommended sites and literature. It is important to know how

both classes regulate gene expression (miRNAs in the nucleus mRNA binding;

lncRNAs much more complex, for example in the nucleus and cytoplasm RNAs and

proteins, but also chromatin and histone modifying) and how to analyze them.

(b) Please have a look at the recommended pages. Then please also our work: Kunz M

et al. (2015) 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 and Kunz M

et  al. (2016) Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics

Analysis to the Development of Non-Invasive Diagnostic Tools. Genes (Basel). 2016

Dec 26; 8(1). pii: E8. https://doi.org/10.3390/genes8010008.

(c) To do this, look at the recommended sites, for example, miRNA-132, miRNA-212 and

miRNA-7 can be found. It is important to see that there are differences between the

targets due to the different algorithms. Therefore, always know about the algorithms

and parameters, compare programs and preferably choose common hits (if available,

use experimentally validated hits).

20.3

Genomes – Molecular Maps of Living Organisms

Question 3.1

For this you should know: 3.2 billion base pairs, about 23,700 genes, 2–3% of the genome

for protein reading frames, most of it is “ballast” (selfish DNA, LINE and SINE). Best to

read the book chapter again.

20  Solutions to the Exercises