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Task 1.9

What is a dot plot and what can I use it for (hint: look up this software on the internet)?

Task 1.10

Example: Dotplot by hand.

1. By hand, perform a dot plot of the word BIOINFORMATICS to compare the word

with itself.

2. Use software (e.g., Dotter [https://sonnhammer.sbc.su.se/Dotter.html], JDotter

[https://athena.bioc.uvic.ca/virology-­ca-­tools/jdotter/], or Cheetah [https://mips.

gsf.de/services/analysis/gepard]) and perform a dot plot of the following sequence

with yourself:

>unknownsequence 1.10

PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQI

LIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Useful Tools and Web Links

Perl

https://www.perl.org/

Java

https://www.oracle.com/technetwork/java/index.html

Python

https://www.python.org/

C++

https://www.cplusplus.com/

R

https://www.r-­project.org/

BLAST

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

PDB

https://www.rcsb.org/pdb/home/home.do

BioNumbers

https://bionumbers.hms.harvard.edu/

PubMed

https://www.ncbi.nlm.nih.gov/pubmed/

EBI

https://www.ebi.ac.uk/services

DDBJ

https://www.ddbj.nig.ac.jp

ExPASy

https://www.expasy.org

PROSITE

https://prosite.expasy.org

SWISS-MODEL

https://swissmodel.expasy.org

MODELLER

https://salilab.org/modeller/tutorial/

QUARK

https://zhanglab.ccmb.med.umich.edu/QUARK/

AnDom

https://andom.bioapps.biozentrum.uni-­wuerzburg.de/

index_new.html

Literature

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

215(3):403–410

Antiretroviral Therapy Cohort Collaboration (2008) Life expectancy of individuals on combination

antiretroviral therapy in high-income countries: a collaborative analysis of 14 cohort studies.

Lancet 372(9635):293–299. https://doi.org/10.1016/S0140-­6736(08)61113-­7

Literature