Piipari_iMotif_BOSC2009

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Matias Piipari presented iMotifs, a sequence motif viewer and editor for the Mac. The goals of iMotifs are to make motif analysis easy for biologists and reuse existing tools. iMotifs includes the NestedMICA motif discovery suite and other analysis tools. It allows viewing, editing, and discovering motifs from uploaded sequences. iMotifs is written in Objective-C, uses the xms-cocoa motif library, is multithreaded, and works on Intel and PowerPC Macs. Future plans include integrating more analysis tools.

Technology Spiritual

Matias Piipari
Supervised by Tim Hubbard and Thomas Down

BOSC 2009

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 motif analysis easy enough for a biologist

Saturday, 27 June 2009

• 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

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

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

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

• Written in Objective-C 2.0 (requires Leopard)

Saturday, 27 June 2009

Under the hood

• Written in Objective-C 2.0 (requires Leopard)

• Includes a sequence motif library xms-cocoa

Saturday, 27 June 2009

Under the hood

• Written in Objective-C 2.0 (requires Leopard)

• Includes a sequence motif library xms-cocoa

• Multithreaded

Saturday, 27 June 2009

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

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 tool you would like to have
integrated to iMotifs?
Come talk with me (or msg matias.piipari@gmail.com)

Saturday, 27 June 2009

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Piipari_iMotif_BOSC2009

1. Matias Piipari Supervised by Tim Hubbard and Thomas Down BOSC 2009 Saturday, 27 June 2009

2. Saturday, 27 June 2009

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

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. • 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. • 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. • 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. What does it look like? Saturday, 27 June 2009

9. Search by consensus Saturday, 27 June 2009

10. Search by keyword(s) Saturday, 27 June 2009

11. Editing functions Saturday, 27 June 2009

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

13. Quicklook Saturday, 27 June 2009

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. Auto updates Saturday, 27 June 2009

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

17. Motif multiple alignment Saturday, 27 June 2009

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

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

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

21. Under the hood Saturday, 27 June 2009

22. Under the hood • Written in Objective-C 2.0 (requires Leopard) Saturday, 27 June 2009

23. Under the hood • Written in Objective-C 2.0 (requires Leopard) • Includes a sequence motif library xms-cocoa Saturday, 27 June 2009

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. 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. 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. Future Saturday, 27 June 2009

28. Future • More analysis tools: scanning, motif hit P-value calculation Saturday, 27 June 2009

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. 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

Piipari_iMotif_BOSC2009

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