Basic Local Alignment Search Tool by lsNgb9V

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									  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_597750.1|
  Coat protein [Tobacco mosaic
              virus]
MSYSITTPSQFVFLSSAWADPIE
LINLCTNALGNQFQTQQARTVV
QRQFSEVWKPSPQVTVRFPDS
DFKVYRYNAVLDPLVTALLGAFD
TRNRIIEVENQANPTTAETLDAT
RRVDDATVAIRSAINNLIVELIRG
TGSYNRSSFESSSGLVWTSGPA
 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

								
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