Current Tasks

Genome Query 0.1 (deadline: 17 March)

• Search algorithms:
  • KMP
  • Suffix arrays (Victor)
  • K-mers (Andrew)
• Annotations are used to get more precised location:
  • search in genes
  • protein id
  • exons & introns (Kate)
• UI:
  • on the fly error checking (Alexey K.)
  • better layout for info/show/count/find results (Vlad O.)
  • improve help layout: see current right side help (Natalya 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 (Andrew)
• Inexact search
• BLAST (Vlad O.)

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

• repeats
• locuses

Parser

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

TODO:

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