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NGS Bioinformatics Workshop 1.4 Tutorial - Comparative Sequence Analysis and Visualization

NGS Bioinformatics Workshop 1.4 Tutorial - Comparative Sequence Analysis and Visualization. March 29th, 2012 IRMACS 10900 Facilitator: Richard Bruskiewich Adjunct Professor, MBB. Tutorial Work Flow. Gene Family Analysis Select a seed sequence of interest

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NGS Bioinformatics Workshop 1.4 Tutorial - Comparative Sequence Analysis and Visualization

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  1. NGS Bioinformatics Workshop1.4 Tutorial - Comparative Sequence Analysis and Visualization March 29th, 2012 IRMACS 10900 Facilitator: Richard Bruskiewich Adjunct Professor, MBB

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

  3. 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

  4. Visualize and analyze the sequences… • Obtain JalView (the easy way – Java web start) http://www.jalview.org/download.html

  5. 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)

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