340

Question 11.22

The TMHMM server link is: https://www.cbs.dtu.dk/services/TMHMM/. Here, any

sequence can be seen by simply pasting it into the question form in terms of transmem­

brane helices including graphics for the extra- or intracellular loops.

Question 11.23

The NucPred link is: https://www.sbc.su.se/~maccallr/nucpred/. Here I can determine all

nuclear localization signals. There is also a database LocSigDB, from which one can

derive many nuclear localization signals.

Question 11.24

The SignalP server link is: https://www.cbs.dtu.dk/services/SignalP/. Here, different neu­

ronal networks are combined to achieve the best possible prediction (for gram-negative

and -positive bacteria and eukaryotes).

Question 11.25

The PROSITE server link is: https://prosite.expasy.org/scanprosite/. The PROSITE motifs

also specify catalytic residues, protein modifications as well as typical amino acid residue

combinations for enzyme families and a range of localization motifs and interaction motifs.

Question 11.26

The ELM server plays all this back in bundled form. It retrieves several programs that are

installed there, i.e. it is a meta server (https://elm.eu.org).

Question 11.27

The link is: https://geneontology.org. A distinction is made between molecular function

(MF), biological process (BP) and cellular compartment (CC).

Questions 11.28 and 11.29

Cytoscape can be found at: https://www.cytoscape.org. Downloadable e.g. from: https://

www.cytoscape.org/download.php. Protein networks are read in and can then be further

analyzed by suitable subprograms (plugins) (see Sect. 20.5). BiNGO (https://apps.cyto­

scape.org/apps/bingo) calculates overrepresentations of biological processes and signaling

pathways (GO terms). Please also have a look at the tutorial section.

20  Solutions to the Exercises