334

Question 10.5

• Parsimony: The phylogenetic tree is calculated in such a way that the observed diver­

sity from the (not observed, but only calculated) precursor sequences is correctly repro­

duced with as little parsing as possible.

• ML, Maximum likelihood the phylogenetic tree is calculated as it probably has been

(single probabilities for each nucleotide exchange are considered). Calculation point

out, ideally take the same FASTA multisequence file.

Question 10.6

Take the NCBI download and also the taxonomy option of BLAST. First use a keyword

search to find the HI virus together with the complete polymerase sequence, e.g.

HIV1 human;

https://www.ncbi.nlm.nih.gov/protein/?term=HIV1+and+human+and+polymerase+co

mplete. Is so already feasible. But if you, for example, simply take HIV and protein and

human as search terms, then you can search yourself to death with so many hits.

They then find for man:

>gi|1906384|gb|AAB50259.1| pol polyprotein (NH2-terminus

uncertain) [Human immunodeficiency virus 1]

M S L P G R W K P K M I G G I G G F I K V R Q Y D Q I L I E I C G H K A

IGTVLVGPTPVNIIGRNLLTQIGCTLNFPISPIETVPVKLKPGMDGPKVKQW

P L T E E K I K A L V E I C T E M E K E G K I S K I G P E N P Y N T P V F A

I K K K D S T K W R K L V D F R E L N K R T Q D F W E V Q L G I P H P A G

L K K K K S V T V L D V G D A Y F S V P L D E D F R K Y T A F T I P S I N N E T

P G I R Y Q Y N V L P Q G W K G S P A I F Q S S M T K I L E P F R K Q N P D I V I Y Q

Y M D D L Y V G S D L E I G Q H R T K I E E L R Q H L L R W G L T T P D K K H Q K

E P P F L W M G Y E L H P D K W T V Q P I V L P E K D S W T V N D I Q K L V

G K L N W A S Q I Y P G I K V R Q L C K L L R G T K A L T E V I P L T E E A E L E L A

E N R E I L K E P V H G V Y Y D P S K D L I A E I Q K Q G Q G Q W T Y Q I Y Q E P F

K N L K T G K Y A R M R G A H T N D V K Q L T E A V Q K I T T E S I V I W G K T

P K F K L P I Q K E T W E T W W T E Y W Q A T W I P E W E F V N T P P L V K L

W Y Q L E K E P I V G A E T F Y V D G A A N R E T K L G K A G Y V T N R G R Q

K V V T L T D T T N Q K T E L Q A I Y L A L Q D S G L E V N I V T D S Q Y A L G I

I Q A Q P D Q S E S E L V N Q I I E Q L I K K E K V Y L A W V P A H K G I G G N E

Q V D K L V S A G I R K V L F L D G I D K A Q D E H E K Y H S N W R A M A S D F

N L P P V V A K E I V A S C D K C Q L K G E A M H G Q V D C S P G I W Q L D C T

H L E G K V I L V A V H V A S G Y I E A E V I P A E T G Q E T A Y F L L K L A G R W

P V K T I H T D N G S N F T G A T V R A A C W W A G I K Q E F G I P Y N P Q S Q G

V V E S M N K E L K K I I G Q V R D Q A E H L K T A V Q M A V F I H N F K R K G G

I G G Y S A G E R I V D I I A T D I Q T K E L Q K Q I T K I Q N F R V Y Y R D S R N P L

W K G P A K L L W K G E G A V V I Q D N S D I K V V P R R K A K I I R

DYGKQMAGDDCVASRQDED

20  Solutions to the Exercises