Genome Query 0.1

  • Search algorithms:
    • (tick) KMP
    • (lightbulb) Suffix arrays (Victor)
    • (lightbulb) K-mers (Andrew)
    • (lightbulb) BLAST (Vlad O.)
  • Annotations are used to get more precised location:
    • (tick) search in genes
    • (lightbulb) protein id (Kate)
    • (lightbulb) exons & introns (Kate)
  • UI:
    • on the fly error checking (Alexey K.)
    • improve help layout: see current right side help (Alexey K.)
    • show sample queries on startup page (Alexey K.)
  • Other:
    • ability to stop long running tasks (Vlad R.)
    • preprocessing, sequence condensed structure (Vlad R.)

Backlog

Search algorithms:

  • Compressed Suffix arrays (Victor)
  • Inexact search

Annotations are used to get more precised location: (Kate) in progress

  • repeats
  • locuses

Parser

  • (lightbulb) inexact search syntax (Alexey A.)
  • (lightbulb) regular expressions (Alexey A.)
  • (question) parsing on client side
  • (question) sytax for search by shift before/after gene

TODO:

  • Use issue tracker!
  • on the fly syntax check (question) client side with better error recovery (question)
  • task estimation time based on algorithm used
  • better instant input validation
  • think about result layout
  • HISTORY of queries















(red star) - Must have feature
(blue star) - Nice to have feature

(question) - Under Investigation
(lightbulb) - In Progress
(tick) - Feature Implemented