GMOD Online Training 2014/WebApollo Tutorial

Using WebApollo

WebApollo is a web-based application, so the only requirement to use it is a web browser. It has been tested with Chrome, Firefox, and Safari. It has not been tested with Internet Explorer.

A WebApollo demo with the Pythium data has been set up on the virtual machine. We'll use the demo to view WebApollo's functionality.

Point your browser to http://ec2-##-##-##-##.compute-1.amazonaws.com:8080/WebApolloDemo.
(e.g., http://ec2-184-73-92-243.compute-1.amazonaws.com:8080/WebApolloDemo).

The user name and password are both demo.

We only have one contig to work with. Click on the scf1117875582023 link.

• Annotation track
• Add evidence tracks (maker, snap_masked, blastn, blastx, est2genome, protein2genome, BAM alignments)
• Moving around the contig
• Go to region scf1117875582023:629476..633770
• Selection
  • Edge matching
• Create annotation
  • Drag-n-drop
• Delete exon (notice the change in CDS)
• Add exon
• Non-canonical splice sites (GT / AG)
• Zoom to base
• DNA track
  • Highlighting
  • 6-frame translation
• DNA sequence insertion, deletion, substitution
• Zoom back out
• Change exon boundaries
• Merge (exons, transcripts)
• Split (exons, transcripts)
• Make intron
• Duplicate
• Set translation start

• Realtime client updating

• History

• Information editor

• Get sequence

• Sequence searching