42

Task 3.2

Describe what is meant by annotation or reannotation of a genome.

Task 3.3

Name and describe different sequencing techniques.

Task 3.4

Describe important steps in genome sequencing (also address bioinformatics challenges or

important hurdles). Do you know any important pioneers of genome sequencing?

Task 3.5

Think about the bioinformatics requirements/challenges of ever-improving sequencing

techniques, but also associated hurdles/limitations.

Task 3.6

Name and describe databases where you can find information about the genome.

Task 3.7

Explain how to bioinformatically screen a promoter sequence for transcription factor bind­

ing sites (name and briefly describe software/databases). What are the advantages of com­

paring e.g. several software/databases?

Task 3.8

Develop a simple program that reads in a promoter sequence, examines it for transcription

factor binding sites, and outputs the result back. What parts would this program consist of?

Also consider what challenges and sources of error this program would have to deal with.

Task 3.9

Analyze a sample RNA sequence:

Using the following sequence, perform a promoter search for possible transcription

factor binding sites using ALGGEN PROMO software (https://alggen.lsi.upc.es/cgi-­bin/

promo_v3/promo/promoinit.cgi?dirDB=TF_8.3):

>FP018429 BRCA1_1

TTCCAAGGAACAGTGTGGCCAAGGCCTTTCGTTCCGCAATGCATGTTGGAAATAGTAGTTCTT

T C C C T C C A C C T C C C A A C A A T C C T T T T A T T T A C C T A A A C T G G A G A C C T C C A

T T A G G G C G G A A A G A G T G G G G T A A T G G G A C C T C T T C T T A A G A C T G C T T T G G A C A C

T A T C T T A C G C T G A T A T T C A G G C C T C A G G T G G C G A T T C T G A C C T T G G T A C A G C

A A T T A C T G T G A C G T A A T A A G C C G C A A C T G G A A G C G T A G A G G C G A G A G G G C G

GGCGCTTTACGGCGAACTCAGGTAGAATTCTTCCTTTTCCGTCTCTTTCTTTTTATGTCACCAGG

G G A G G A C T G G G T G G C C A A C C C A G A G C C C C G A G A G A T G C T A G G C T C T T T C T G T C C C

G C C C T T C C T C T G A C T G T G T C T T G A T T T C C T A T T C T G A G A G G C T A T T G C T C A G C

G G T T T C C G T G G C A A C A G T A A A G C G T G G G A A T T A C A G A T A A A T T A A A A C T G T G G A A

3  Genomes: Molecular Maps of Living Organisms