335

Now use BLAST:

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

Pay attention to the protein BLAST:

https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_

TYPE=BlastSearch&LINK_LOC=blasthome

Paste sequence into question form.

20.8

The phylogenetic tree should now show that the domains are well conserved. For this,

you can look at the alignments in detail (lower part of the BLAST result). But very helpful

is the phylogenetic tree report (click on “Taxonomy Report”). In particular, you will find

all species listed and the number of found, related species sorted by organism groups

(here, of course, because searched with HIV, mainly HIV polymerase sequences).

Question 10.7

Proceed analogously as in 10.6, but here the species richness is much greater, nice fam­

ily tree.

Question 10.8

CLUSTAL has the following link: https://www.ebi.ac.uk/Tools/msa/clustalo/. MUSCLE

can be found here https://www.ebi.ac.uk/Tools/msa/muscle/. For orientation, Parsimony

and ML are referred to here (see Sect. 10.5).

Question 10.9

With a multiple alignment, you can compare multiple sequences and identify similar or

dissimilar regions.

Question 10.10

For this, all you have to do is look closely at the SMART domain analysis website and seek

out the seed alignment. In particular, also look at the conserved and less conserved

residues.

20.10  Understand Evolution Better Applying the Computer