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TheEvergreenStateCollege / bioinformatics

Plant genome sequencing
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How to partially render a suffix tree from db #38

Open learner-long-life opened 2 months ago

learner-long-life commented 2 months ago

Right now the suffix trees produced from the whole genome of 400m characters are too large to be displayed entirely at once in the web UI.

How do we query the DB to get just part of the suffix tree to render? Starting at which subtree node ID and ending where?

learner-long-life commented 2 months ago

The Ukkonen visualizer is open source, feel free to borrow and adapt code from it.

Instead of visualizing a suffix tree from a user-entered input string, we want to visualize a suffix tree that is read from the database. Let's keep track of questions that come up here, such as, what parameters we need to specify for a partial suffix tree, and how to show where the partial suffix tree is in the bigger suffix tree (e.g. a mini-map)

https://github.com/brenden/ukkonen-animation