Current Tasks

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:
  • 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 id
  • exons & introns
• UI:
  • on the fly error checking
  • better layout for info/show/count/find results
  • improve help layout: see current right side help
  • show sample queries on startup page
• Other:
  • ability to stop long running tasks
  • sequence condensed structure
  • preprocessing script

Backlog

Search algorithms:

• (don't need) Compressed Suffix arrays (Andrew)
• BLAST

Parser

• inexact search syntax (Alexey A.)
• regular expressions (Alexey A.)
• parsing on client side
• 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