NGS Bioinformatics Workshop 1.4 Tutorial - Comparative Sequence Analysis and Visualization March 29th, 2012 IRMACS 10900 Facilitator: Richard Bruskiewich.

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NGS Bioinformatics Workshop 1.4 Tutorial - Comparative Sequence Analysis and Visualization March 29th, 2012 IRMACS Facilitator: Richard Bruskiewich Adjunct Professor, MBB

Tutorial Work Flow  Gene Family Analysis  Select a seed sequence of interest  Compile a set of homologous sequences  Visualize and analyse the sequences

Select a seed sequence of interest  Query for a protein sequence of interest from Entrez Compile a set of homologous sequences  Go from Entrez record to using PSIBlast to compile a set of homologous sequences for analysis; download the resulting sequence file

Visualize and analyze the sequences…  Obtain JalView (the easy way – Java web start)

Visualize and analyze the sequences…  Obtain JalView (the easy way – Java web start)  Load the sequence file into JalView  Run MSA as a web service  Display a phylogenetic tree  Retrieve PDB structures  And a lot of other things… (documented)