Similarity, cont’d!

Table of Contents

Similarity, cont’d!

Information from Alignments

Multiple Alignment

Alignment Methods/Programs

MSA Strategy

Running MSA

Clustal W(X) Strategy

Running Clustal W/X

Clustal X Ouptut

Options

Pileup (GCG)

Pileup Output

“The Right Proteins”

“The Right Proteins”

Alignment Interpretation

MACAW

Uses of Alignment

“The Right Proteins”

Motifs vs Alignment

PROSITE

Running PROSITE

BLOCKS

Profile Analysis (GCG)

Protein Analysis Flowchart

Email: staben@pop.uky.edu

Home Page: www.uky.edu/Classes/BIO520/BIO520WWW/

Other information:
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