Page History

Genome Query 1.0

(deadline: 1 June)

• Info
  • SNPs
• Show
  • Protein sequence
• Find/Count
  • Common algorithms interface for KMP, SA, K-mers (Victor, Nadya)
  • Slow inexact search (wildcards M, R, N etc.) (Alexey A.)
  • Wildcards for inexact search (Alexey A.)
  • Protein search through wild-carded DNA search (Alexey A.)
• What
• Other
  • Better layout on browser window resize
  • More crosslinks in result's output (to INFO, SHOW, WHAT queries)
  • Javadoc comments to some classes (Everybody)

Genome Query 0.3 (deadline: 11 May, feature freeze: 10 May)

• Search algorithms:
  • KMP
  • Suffix arrays (Victor)
  • K-mers (Andrew)
  • Fast inexact search (wildcards M, R, N etc.)
  • WHAT command fast implementation
  • Real-time results
  • Inexact search (at least k mismatches)
  • search by shift before/after gene (Alexey A.)
• Parser:
• UI:
  • History of queries
  • FIND/COUNT result grouping based on locations in query (extLoc)
• Annotation
  • repeats
• Other:
  • Javadoc comments to all classes (Everybody)

Genome Query 0.2 (deadline: 20 April, feature freeze: 13 April)

• Search algorithms:
  • K-mers for all chromosomes
  • WHAT command slow implementation
• Annotations:
  • locuses
• Parser:
  • WHAT command
• Other:
  • Javadoc comments to some classes (Everybody)

Genome Query 0.1 (deadline: 23 March)

• Search algorithms:
  • KMP
  • Suffix arrays for all chromosomes
• Annotations are used to get more precised location:
  • search in genes
  • protein  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.)
  • preprocessing script

Backlog

Search algorithms:

• (don't need) 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
• find in protein-coding genes (Alexey A.)
• find in exons, introns, genes, genome (Alexey A.)
• alternatives for nucleotides (Alexey A.)

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