Molecular Evidence
Using DNA, RNA or Protein
Sequences to Classify Organisms
Creating a Phylogenetic
Tree
from DNA (or RNA)
Sequences
Using Computer Programs
Steps
1. Obtain a set of related sequences.
a. Isolate and sequence DNA from a group of organisms
Or
b. Use BLAST to find a set of related sequences from a group of
organisms whose DNA has been previously sequenced
2. Use Clustal W to align the sequences.
3. Use DrawGram to construct the most
likely phylogenetic tree.
Basic Local Alignment
Search Tool
BLAST
BLAST is the most
commonly used
bioinformatics tool!
BLAST helps you to find
homologous genes and proteins
Homologous Genes
Have a common ancestor (they’re
related)
Have similar structures
Have similar functions
What does BLAST do?
BLAST compares sequences
• BLAST takes a query sequence
• Compares it with one or millions of sequences
in the Genbank databases
• Lists those that appear to be similar to the query
sequence
– The “hit list”
• Tells you why it thinks they are homologs
For Example:
Can We Use The Coat
Protein of the Tobacco
Mosaic Virus (TMV)To Help
Us to Classify This Virus?
TMV Coat Protein is the Query
Sequence
The TMV Coat Protein
Sequence
>gi|19263363|ref|NP_59775
0.1| Coat protein
[Tobacco mosaic virus]
MSYSITTPSQFVFLSSAWADPIELI
NLCTNALGNQFQTQQARTVVQRQFS
EVWKPSPQVTVRFPDSDFKVYRYNA
VLDPLVTALLGAFDTRNRIIEVENQ
ANPTTAETLDATRRVDDATVAIRSA
INNLIVELIRGTGSYNRSSFESSSG
LVWTSGPAT
BLAST “Hit List” of
Proteins Related to the
Tobacco Mosaic Virus
Coat Protein
BLAST compares one
sequence with other
sequences
In order to construct a
phylogenetic tree, we need to
compare all members of a
group of sequences.
Why Use Clustal W?
• In order to compare a group of related
sequences for similarity, they must be
lined up, or aligned in a chart called a
multiple alignment
A Multiple Alignment
Constructed by Clustal W
How do I interpret the
results of a CLUSTAL W
alignment?
Programs, such as DrawGram,
are used to compare the
sequences in the alignment and
present them in a visually
appealing form
Use DrawGram to
Construct the Most Likely
Phylogenetic Tree
DrawGram
• Analyzes the aligned sequences for
similarities and differences
• Constructs the most likely phylogenetic
tree that reflects the comparison of the
sequences
A Rooted Phylogenetic Tree
Drawn by DrawGram
Constructed from a multiple
alignment of coat proteins from
several plant viruses