Matias Piipari
                         Supervised by Tim Hubbard and Thomas Down

                                       ...
Saturday, 27 June 2009
• Sequence motif viewer and editor for the Mac




Saturday, 27 June 2009
• Sequence motif viewer and editor for the Mac
                 • Philosophy:
                         •   let’s make moti...
• Sequence motif viewer and editor for the Mac
                 • Philosophy:
                         •   let’s make moti...
• Sequence motif viewer and editor for the Mac
                 • Philosophy:
                         •   let’s make moti...
• Sequence motif viewer and editor for the Mac
                 • Philosophy:
                         •   let’s make moti...
What does it look like?




Saturday, 27 June 2009
Search by consensus




Saturday, 27 June 2009
Search by keyword(s)




Saturday, 27 June 2009
Editing functions




Saturday, 27 June 2009
wt*, it’s Mac only?




Saturday, 27 June 2009
Quicklook




Saturday, 27 June 2009
PDF output
                         motif0

                                  TTC AAA
                                  C
...
Auto updates




Saturday, 27 June 2009
It’s not just a viewer.




Saturday, 27 June 2009
Motif multiple alignment




Saturday, 27 June 2009
Best hits between motif sets
                           (and empirical P-values)




Saturday, 27 June 2009
Motif discovery with
                         FASTA drag & drop




Saturday, 27 June 2009
Retrieve sequences for motif
                           discovery from Ensembl




Saturday, 27 June 2009
Under the hood




Saturday, 27 June 2009
Under the hood

                         •   Written in Objective-C 2.0 (requires Leopard)




Saturday, 27 June 2009
Under the hood

                         •   Written in Objective-C 2.0 (requires Leopard)

                         •   I...
Under the hood

                         •   Written in Objective-C 2.0 (requires Leopard)

                         •   I...
Under the hood

                         •   Written in Objective-C 2.0 (requires Leopard)

                         •   I...
Under the hood

                         •   Written in Objective-C 2.0 (requires Leopard)

                         •   I...
Future




Saturday, 27 June 2009
Future

        • More analysis tools:
                scanning, motif hit P-value calculation




Saturday, 27 June 2009
Future

        • More analysis tools:
                scanning, motif hit P-value calculation
        • Do you have a too...
Future

        • More analysis tools:
                scanning, motif hit P-value calculation
        • Do you have a too...
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Piipari_iMotif_BOSC2009

  1. 1. Matias Piipari Supervised by Tim Hubbard and Thomas Down BOSC 2009 Saturday, 27 June 2009
  2. 2. Saturday, 27 June 2009
  3. 3. • Sequence motif viewer and editor for the Mac Saturday, 27 June 2009
  4. 4. • Sequence motif viewer and editor for the Mac • Philosophy: • let’s make motif analysis easy enough for a biologist Saturday, 27 June 2009
  5. 5. • Sequence motif viewer and editor for the Mac • Philosophy: • let’s make motif analysis easy enough for a biologist • reuse and bundle existing tools where possible Saturday, 27 June 2009
  6. 6. • Sequence motif viewer and editor for the Mac • Philosophy: • let’s make motif analysis easy enough for a biologist • reuse and bundle existing tools where possible • Built-in NestedMICA motif discovery suite Saturday, 27 June 2009
  7. 7. • Sequence motif viewer and editor for the Mac • Philosophy: • let’s make motif analysis easy enough for a biologist • reuse and bundle existing tools where possible • Built-in NestedMICA motif discovery suite • Other built-in analysis tools will hopefully follow Saturday, 27 June 2009
  8. 8. What does it look like? Saturday, 27 June 2009
  9. 9. Search by consensus Saturday, 27 June 2009
  10. 10. Search by keyword(s) Saturday, 27 June 2009
  11. 11. Editing functions Saturday, 27 June 2009
  12. 12. wt*, it’s Mac only? Saturday, 27 June 2009
  13. 13. Quicklook Saturday, 27 June 2009
  14. 14. PDF output motif0 TTC AAA C A G GG CA AT C G A T G C TTG CT GC motif1 G TTTGCC CC A ACA G G ACTTC TG A AG G A T motif2 T G CC A A GAT T G A C GC A C T A T GG GTCA C TTT ACC GA G motif3 AAAACT GGC T CC T TTGGAC G GC T AC G A T motif4 TTT C G AA C G C A G T G CT A CAG G A C G TC T A A TC GT CG A Saturday, 27 June 2009
  15. 15. Auto updates Saturday, 27 June 2009
  16. 16. It’s not just a viewer. Saturday, 27 June 2009
  17. 17. Motif multiple alignment Saturday, 27 June 2009
  18. 18. Best hits between motif sets (and empirical P-values) Saturday, 27 June 2009
  19. 19. Motif discovery with FASTA drag & drop Saturday, 27 June 2009
  20. 20. Retrieve sequences for motif discovery from Ensembl Saturday, 27 June 2009
  21. 21. Under the hood Saturday, 27 June 2009
  22. 22. Under the hood • Written in Objective-C 2.0 (requires Leopard) Saturday, 27 June 2009
  23. 23. Under the hood • Written in Objective-C 2.0 (requires Leopard) • Includes a sequence motif library xms-cocoa Saturday, 27 June 2009
  24. 24. Under the hood • Written in Objective-C 2.0 (requires Leopard) • Includes a sequence motif library xms-cocoa • Multithreaded Saturday, 27 June 2009
  25. 25. Under the hood • Written in Objective-C 2.0 (requires Leopard) • Includes a sequence motif library xms-cocoa • Multithreaded • Works on PPC, i386, x86-64 (Universal Binary) Saturday, 27 June 2009
  26. 26. Under the hood • Written in Objective-C 2.0 (requires Leopard) • Includes a sequence motif library xms-cocoa • Multithreaded • Works on PPC, i386, x86-64 (Universal Binary) • LGPL licensed Saturday, 27 June 2009
  27. 27. Future Saturday, 27 June 2009
  28. 28. Future • More analysis tools: scanning, motif hit P-value calculation Saturday, 27 June 2009
  29. 29. Future • More analysis tools: scanning, motif hit P-value calculation • Do you have a tool you would like to have integrated to iMotifs? Come talk with me (or msg matias.piipari@gmail.com) Saturday, 27 June 2009
  30. 30. Future • More analysis tools: scanning, motif hit P-value calculation • Do you have a tool you would like to have integrated to iMotifs? Come talk with me (or msg matias.piipari@gmail.com) • Available at http://imotifs.pearcomp.com Saturday, 27 June 2009

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