Tools

Tools available for data analysis

BLAST - search the genome

JBrowse - view genome annotations

There is currently one annotation track under display:

  • "Maker_annotations" is based on the output from the annotation pipeline Maker. It was trained by feeding the output of the CEGMA analysis into SNAP, which produced a Hidden Markov Model that was used in Maker. Repetitive regions and ab-initio predicted genes are visible.

How to navigate in JBrowse

From "Available Tracks" on the left hand side, drag the tracks of interest onto the main panel to activate it (or double-click on the track label).
Zoom in and out using the magnifying glasses in the middle of the tool bar.
Move along the length of a sequence by dragging the red sliding window at the very top, by hitting the respective arrows in the tool bar, or by moving the main panel directly.
To view a different scaffold, just type its name in the white panel in the tool bar and hit "Go" (or press enter).
For more information visit the JBrowse webpage or hit the "?Help" button in the upper right corner of the browser interface