Genome Query 0.1 (deadline: 17 March)

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

Genome Query 0.2 (deadline: 1 April)

  • Search algorithms:
    • Inexact search (at least k mismatches)
    • WHAT command simple implementation
  • Annotations:
    • repeats
    • locuses
  • Parser:
    • WHAT command
  • UI:
    • Better layout on browser window resize
    • FIND/COUNT result grouping based on locations in query (extLoc)
    • More crosslinks in result's output (to INFO, SHOW, WHAT queries)
  • Other:
    • Javadoc comments to all classes (Everybody)

Backlog

Search algorithms:

  • (don't need) Compressed Suffix arrays (Andrew)
  • (lightbulb) BLAST (Vlad O.)

Parser

  • (tick) inexact search syntax (Alexey A.)
  • (tick) 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