The document discusses creating a pipeline for EST analysis by assembling EST reads into contigs, detecting SNPs, and displaying results online. Several tools are proposed, including MIRA for assembly but it is noted to be slow, poorly documented, and buggy. The pipeline will parse outputs from tools like BLAST, PFAM, and ORF prediction into a structured database. It has created the pipeline, started analyzing data and filling the database, and next steps are to wait for MIRA and add an SNP parser.

1. Dr. Stickle
an EST-Database

2. Dr. Stickle
an EST-Database

3. The Goal

4. The Goal
• Creating a pipeline for EST-Analysis

5. The Goal
• Creating a pipeline for EST-Analysis
• Displaying the results via an online
framework

6. wtf is a pipeline?

7. Different steps of analysis performed in an
automated fashion
wtf is a pipeline?

8. wtf is a pipeline?
Different steps of analysis performed in an
automated fashion

9. Analysis:

10. ✓Assembly of EST-Reads into contigs
✓SNP-Detection
MIRA
But:
★Takes ages
★not well documented
★buggy

11. ✓Assembly of EST-Reads into contigs
✓SNP-Detection
MIRA
But:
★Takes ages
★not well documented
★buggy

12. ✓Assembly of EST-Reads into contigs
✓SNP-Detection
MIRA
But:
★Takes ages
★not well documented
★buggy

13. MIRA
✓Assembly of EST-Reads into contigs
✓SNP-Detection
But:
★Takes ages
★not well documented
★buggy

14. MIRA
✓Assembly of EST-Reads into contigs
✓SNP-Detection
But:
★Takes ages
★not well documented
★buggy

15. MIRA
✓Assembly of EST-Reads into contigs
✓SNP-Detection
But:
★Takes ages
★not well documented
★buggy

16. MIRA
✓Assembly of EST-Reads into contigs
✓SNP-Detection
But:
★Takes ages
★not well documented
★buggy

17. SNPs ORFs Contigs BLAST
MIRA
PFAM BLAST2GO

18. MIRA
SNPs ORFs Contigs BLAST
PFAM BLAST2GO

19. MIRA
Contigs
SNPs ORFs BLAST
PFAM BLAST2GO

20. MIRA
Contigs
SNPs ORFs BLAST
PFAM BLAST2GO

21. MIRA
Contigs
SNPs ORFs BLAST
PFAM BLAST2GO

22. MIRA
Contigs
SNPs ORFs BLAST
PFAM BLAST2GO

23. MIRA
Contigs
SNPs ORFs BLAST
PFAM BLAST2GO

24. BLAST
Basic Local Alignment Search Tool

25. BLAST
Basic Local Alignment Search Tool

26. BLAST
Basic Local Alignment Search Tool
• Standard for searching sequences against
a database

27. BLAST
Basic Local Alignment Search Tool
• Standard for searching sequences against
a database
• emphasizes speed over sensitivity

28. BLAST
Basic Local Alignment Search Tool
• Standard for searching sequences against
a database
• emphasizes speed over sensitivity

29. BLAST
Basic Local Alignment Search Tool
• Standard for searching sequences against
a database
• emphasizes speed over sensitivity

30. BLAST
Basic Local Alignment Search Tool
• Standard for searching sequences against
a database
• emphasizes speed over sensitivity

31. Tools
gene ontology
Blast2GO
mapping
open reading frame
ORF
prediction
PFAM domain annotation

32. Blast2GO

33. Tools
gene ontology
Blast2GO
mapping
open reading frame
ORF
prediction
PFAM domain annotation

34. ORF

35. Tools
gene ontology
Blast2GO
mapping
open reading frame
ORF
prediction
PFAM domain annotation

36. PFAM

38. Ugly *.ace-output generated via MIRA

39. What we‘ve got here:

40. What we‘ve got here:
•Different tools
•many different output-files

41. What we‘ve got here:
•Different tools
•many different output-files
What we want:
a structured database containing all the
information

42. How to parse
Class «Parser»
•Function BLAST-Parser
•Function PFAM-Parser
•Function FASTA-Parser
•...
Data
Script
•read input
•use parser
•insert db

43. How to parse
Class «Parser»
•Function BLAST-Parser
•Function PFAM-Parser
•Function FASTA-Parser
•...
Data
Script
•read input
•use parser
•insert db

44. How to parse
Class «Parser»
•Function BLAST-Parser
•Function PFAM-Parser
•Function FASTA-Parser
•...
Data
Script
•read input
•use parser
•insert db

45. How to parse
Class «Parser»
•Function BLAST-Parser
•Function PFAM-Parser
•Function FASTA-Parser
•...
Data
Script
•read input
•use parser
•insert db

46. How to parse
Data
Class «Parser»
•Function BLAST-Parser
•Function PFAM-Parser
•Function FASTA-Parser
•... Script
•read input
•use parser
•insert db
Database

47. >abc_123
agtagtacgtacgtggacgtatgact
>def_456
agtagtacgtacgtggacgtatgact

51. Summary & Results

52. Summary & Results
•created the pipeline
•analysed data
•started filling the database

53. Summary & Results
•created the pipeline
•analysed data
•started filling the database
To be done
•wait for MIRA
•SNP-parser

54. thx to:
•Marvin, for «time till scooter» and sending us to Lothar
•Lothar, for providing always friendly and calm advice
•Suse, for actually having used MIRA at least once
•Andrew, for Andreas
•Andreas, for Andrew
•Bastien Chevreux, for not fixing those damn bugs in MIRA

55. k,thx,bai

56. Dr. Iglo

57. Dr. Iglo