BIO 332 BIOINFORMATICS
EXERCISE 3: Retrieving and comparing amino acid sequences from different
species
Name: ______________________________________
This exercise combines Case Study 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. Copy and paste the FASTA
output and paste in a word processor or text editor.
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 whale (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?