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2 Οκτ 2013 (πριν από 4 χρόνια και 3 μήνες)

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BIO 332
BIOINFORMATICS

EXERCISE 3
:

Retrieving and comparing amino acid sequences from different
species



Name: ______________________________________



This exercise combines Case Stud
y 1.3 and Case Study 1.4 in Lesk (2008) with
modifications.
Your
report will be presented as a short scientific paper with
INTRODUCTION, METHODS, RESULTS, and DISCUSSION.
The issue revolves
around the question of what species is most closely related to Minke whales
,
given the representatives from

two mammalian groups;

Placentals and
Marsupials

(Figure out yourself which is which
)
.
Present your alignment (output in
RESULTS), and your answers to the questions in the DISCUSSION.


The
first
exercise involves retrieving amino acid sequence of horse pancreatic
ribonuclease.

Go to the ExPASy server at the Swis Instittute for Bioinformaics (http:
//expasy.org) and type


horse pancreatic ribonuclease


Under Sequences, click FASTA to generate the entry. C
opy and paste the
FASTA

output and paste
in a word processor or text edi
tor.



What is the geninfo number?



What is the source database?



What is the literature citation where the sequence was first published?




Retrieve

amino acid sequences from
minke whal
e (Baalaenoptera acutorostrata)
,
red kangaroo (Macropus rufus),
and naked mole rat (Heterocephalus glaber).


Copy your dataset of total five

species and paste into the
multiple sequence
alignment
program:




CLUSTAL
-
W
http://www.ebi.ac.uk/clustalw/

or

T
-
Coffee

http: //www.ch.embnet.org/software/TCoffee.html


Figure 1.
Copy and paste your multiple alignment output into the box below














































Fill in the Table below:


Table 1.
Number of identical residues in aligned
ribonuclease among 5 species of
mammals


Pairwise comparison

Number of identical
residues between
pairs of species

Horse and Minke Whale


Minke whale and kangaroo


Minke whale and naked mole rat


Kangaroo and naked mole rat


Horse and naked mole
rat


Kangaroo and horse



Q:
Based on pairwise comparison between 4 species, what species is most closely
related to Minke whale?




Q:
Which species is most distant to the Minke whale?