43

CCCCTTTCCTCGGCTGCCGCCAAGGTGTTCGGTCCTTCCGAGGAAGCTAAGGCCGCGTTGGG

GTGAGACCCTCACTTCATCCGGTGAGTAGCACCGCGTCCG

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

(A) ALGGEN PROMO does not find transcription factor binding sites in the DNA

sequence.

(B) All hits found are also actual transcription factor binding sites, so in each case it

is sufficient to predict them bioinformatically only.

(C) Transcription factors bind to DNA motifs, I can predict these bioinformatically.

(D) ALGGEN PROMO finds a transcription factor binding site for NF-AT2 in the

promoter (with the “matrix dissimilarity rate” setting of 15). I can then use this

information for further experimental studies, such as whether NF-AT2 has an

influence on transcription, in this case of BRCA1.

Task 3.10

Explain a Hidden Markov Model (feel free to use an example).

Useful Tools and Web Links

Pfam

https://pfam.xfam.org/

Rfam

https://rfam.xfam.org/

SMART

https://smart.embl-­heidelberg.de/

ProDom

https://prodom.prabi.fr/prodom/current/html/home.php

UniProt

https://www.uniprot.org/

GenScan

https://genes.mit.edu/GENSCAN.html

HMMER

https://hmmer.org/

SignalP

https://www.cbs.dtu.dk/services/SignalP/

TMHMM

https://www.cbs.dtu.dk/services/TMHMM/

Transfac

https://www.gene-­regulation.com/pub/databases.html

TESS

https://www.cbil.upenn.edu/tess/

MotifMap

https://motifmap.ics.uci.edu/

Alggen Promo

https://alggen.lsi.upc.es/cgi-­bin/promo_v3/promo/promoinit.

cgi?dirDB=TF_8.3

Genomatix

https://www.genomatix.de/

MEME Suite

https://meme-­suite.org/

iRegulon

https://iregulon.aertslab.org/

tRNAscan

https://lowelab.ucsc.edu/tRNAscan-­SE/

Repeat Masker

https://www.repeatmasker.org/

ENCODE

https://www.encodeproject.org

NIH

https://www.genome.gov

Genomic Science

program

https://genomics.energy.gov

Human Genome

Project

https://web.ornl.gov/sci/techresources/Human_Genome/index.

shtml

Ensembl

https://www.ensembl.org/Homo_sapiens/Info/Index

3.4  Exercises for Chap. 3