169

12.3

Exercises for Chap. 12

Task 12.1

Test senseless and meaningful oligonucleotide sequences: By now you already know

BLAST. Now test more precisely which sequences are recognized and which are not:

Compare a sequence from Genbank with a random sequence generated by random key

strokes from the keyboard. Which different types of answers do you get from the server?

What does the E-value mean in the result?

Task 12.2

Search the protein database for words from our language:

(a) Search with a word, such as “DNA” or “JAMES WATSON”.

(b) Which letters never occur in the first letter amino acid code?

(c) What are so-called wobble codons?

Task 12.3

What does the “Universal Code” look like (hint: https://www.ncbi.nlm.nih.gov/Taxonomy/

Utils/wprintgc.cgi)?

Task 12.4

Applied example: Pick out the design of insulin expression for optimal expression in yeast

cells. Put together the differences that directly catch the eye!

Useful Tools and Web Links

GATK

https://software.broadinstitute.org/gatk/guide/

article?id=7869#1.3

BLAST

https://blast.ncbi.nlm.nih.gov/Blast.cgi

UniProt

https://www.uniprot.org/

Literature

Altschul SF, Gish W, Miller W et  al (1990) Basic local alignment search tool. J Mol Biol

215(3):403–410

Bedau MA (2003) Artificial life: organization, adaptation and complexity from the bottom up.

TRENDS Cognitive Sci 7:505–512

Eigen M, Schuster P (1979) The hypercycle: a principle of natural self-organization. Springer, Berlin

Eigen M, Winkler R (1975) Laws of the game: how the principles of nature govern chance. ISBN:

9780691025667 Published: Apr 11, 1993 Princeton University Press.

12.4  Literature