1. Molecular Evidence Using DNA, RNA or Protein Sequences to Classify Organisms

2. Creating a Phylogenetic Tree from DNA (or RNA) Sequences Using Computer Programs

3. 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.

4. Basic Local Alignment Search Tool BLAST

5. BLAST is the most commonly used bioinformatics tool!

6. BLAST helps you to find homologous genes and proteins Homologous Genes Have a common ancestor (they’re related) Have similar structures Have similar functions

7. What does BLAST do?

8. 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

9. 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

10. The TMV Coat Protein Sequence >gi|19263363|ref|NP_597750.1| Coat protein [Tobacco mosaic virus] MSYSITTPSQFVFLSSAWADPIE LINLCTNALGNQFQTQQARTVV QRQFSEVWKPSPQVTVRFPDS DFKVYRYNAVLDPLVTALLGAFD TRNRIIEVENQANPTTAETLDAT RRVDDATVAIRSAINNLIVELIRG TGSYNRSSFESSSGLVWTSGPA T

11. BLAST “Hit List” of Proteins Related to the Tobacco Mosaic Virus Coat Protein

13. 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.

14. 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

15. A Multiple Alignment Constructed by Clustal W

16. 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

17. Use DrawGram to Construct the Most Likely Phylogenetic Tree

18. DrawGram Analyzes the aligned sequences for similarities and differences Constructs the most likely phylogenetic tree that reflects the comparison of the sequences

19. A Rooted Phylogenetic Tree Drawn by DrawGram Constructed from a multiple alignment of coat proteins from several plant viruses