Download Treebuilding_Act

Using the rRNA gene as a molecular marker:
I. Building a phylogenetic tree
Goal: To build the phylogenetic tree for the following sequences:
A: A G C C G T T A A C
B: A C G C G A T A A G
C: T G C C G T A A A C
D: T G C G C T T A A C
E: A C G C G A C A A G
1. Construct a distance matrix: how many differences exist between
each pair?
A
B
C
D
A
X
B
X
X
C
X
X
X
D
X
X
X
X
E
X
X
X
X
E
X
2. Use your distance matrix to build a tree to make a prediction about
how these sequences are related.
II. How are trees constructed of hundreds of sequences at once?
First, the sequences are aligned. To do this for our sequences…
In Firefox
Go to this website: http://www.ebi.ac.uk/Tools/clustalw2/
This is the European Bioinformatics Institute website which offers an
interactive version of a common alignment program called Clustal.
To use this program to align our sample sequences and construct a tree, copy
and paste the following lines into the box where it says:
Enter or paste a set of sequences in any supported format:
>SpA
AGCCGTTAAC
>SpB
ACGCGATAAG
>SpC
TGCCGTAAAC
>SpD
TGCGCTTAAC
>SpE
ACGCGACAAG
(This format is known as FASTA format)
Click on Run to begin your alignment.
The program aligns, creates a distance matrix and draws a tree for you. (as a
cladogram or phylogram). How close was your prediction?
III. What about real genes?
How can we visualize the relationships between our genes and our relatives?
One way is through a tool called Blast.
In Firefox
Go to: http://www.ncbi.nlm.nih.gov/
In search box, type FTO, scroll down in Search menu and choose Protein
Then Search
Choose the Homo sapiens FTO gene.
From right menu under Analyze this sequence, Choose Run Blast
The Blast window will appear with the sequence already entered.
Click Blast (in the lower left corner). Choose Show results in a new window
Click on Distance Tree of Results
Does the tree for this gene reflect the evolutionary positions of well
known organisms?