NGS Bioinformatics Workshop1.4 Tutorial - Comparative Sequence Analysis

and Visualization

March 29th, 2012IRMACS 10900

Facilitator: Richard BruskiewichAdjunct Professor, MBB

Tutorial Work Flow

Gene Family AnalysisSelect a seed sequence of interestCompile a set of homologous sequencesVisualize 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…

http://www.jalview.org/download.html

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 JalViewRun MSA as a web serviceDisplay a phylogenetic treeRetrieve PDB structuresAnd a lot of other things… (documented)