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GNPAnnot Community Annotation System applied to sugarcane BAC clone sequences

GNPAnnot Community Annotation System applied to sugarcane BAC clone sequences. Valentin GUIGNON PAG Sugarcane Genome Sequencing Initiative Sunday, 16 January 2011. >10 studied species. 9 partners. GDEC. Spo. BIVI. What is GNPAnnot. 3 bioinformatics platform. What is GNPAnnot. Goals.

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GNPAnnot Community Annotation System applied to sugarcane BAC clone sequences

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  1. GNPAnnot Community Annotation System applied to sugarcane BAC clone sequences Valentin GUIGNON PAG Sugarcane Genome Sequencing Initiative Sunday, 16 January 2011

  2. >10 studied species 9 partners GDEC Spo BIVI What is GNPAnnot Valentin GUIGNON

  3. 3 bioinformatics platform What is GNPAnnot Valentin GUIGNON

  4. Goals • Automatic annotation pipeline for genes and repeats • Complete manual annotation framework with • Data confidentiality • Inspection of manual annotation • Annotation history • Comparative genomics • Data query and report system Valentin GUIGNON

  5. GNPAnnot Concept Valentin GUIGNON

  6. blastp, tblastn, Interproscan, BBMH, Greenphyl In House Annotation Pipeline Automatic genes structural & functional prediction DNA sequence (BAC) Blastx FGenesH Genome Threader SpliceMachine Eugene HMM STRUCTURAL Eugene FUNCTIONAL Valentin GUIGNON

  7. Repeats Automatic Annotation • Dawg Paws • Repet Valentin GUIGNON

  8. About our Annotation Pipelines Species-specific parameters Sugarcane trained on rice Already in use for full-genoms We can process your sequences Sunday, 16 January 2011 Valentin GUIGNON 8

  9. Portal: http://www.gnpannot.org Valentin GUIGNON

  10. Portal: http://www.gnpannot.org Sunday, 16 January 2011 Valentin GUIGNON 10

  11. Portal: http://www.gnpannot.org Sunday, 16 January 2011 Valentin GUIGNON 11

  12. Portal: http://www.gnpannot.org Sunday, 16 January 2011 Valentin GUIGNON 12

  13. Portal: http://www.gnpannot.org Sunday, 16 January 2011 Valentin GUIGNON 13

  14. Portal: http://www.gnpannot.org Sunday, 16 January 2011 Valentin GUIGNON 14

  15. Portal: http://www.gnpannot.org Sunday, 16 January 2011 Valentin GUIGNON 15

  16. GBrowse Sunday, 16 January 2011 Valentin GUIGNON 16

  17. GBrowse Sunday, 16 January 2011 Valentin GUIGNON 17

  18. GBrowse Sunday, 16 January 2011 Valentin GUIGNON 18

  19. Artemis Sunday, 16 January 2011 Valentin GUIGNON 19

  20. Artemis Sunday, 16 January 2011 Valentin GUIGNON 20

  21. Artemis Sunday, 16 January 2011 Valentin GUIGNON 21

  22. Artemis Validations: # Start/Stop codon validation: -Sh253G12_g190: Start Codon: OK Stop Codon: OK # Sequence validation: -Sh253G12_g190: Length: ERROR: coding sequence length ( 883 bp) is not a multiple of 3! # Introns validation: -Sh253G12_g190 Intron AG Site: ERROR: unrecognized acceptor site (*CA*GAAG at position 62052 from contig sequence begining) between exons 7 and 8! # Mandatory properties management: -Sh253G12_g190: Mandatory properties management: ERROR: missing /functional_completeness qualifier! Mandatory Properties Management: ERROR: missing /inference qualifier! # Gene structure validation: -Sh253G12_g190 (non-obsolete mRNA): OK # Evidence code coherence management: -Sh253G12_g190: Evidence Code Management: WARNING: /evidence_code value should be set for gene Sh253G12_g190! Your changes will be committed to the database and the errors notified above will be reported as qualifiers (when available). Sunday, 16 January 2011 Valentin GUIGNON 22

  23. Artemis Sunday, 16 January 2011 Valentin GUIGNON 23

  24. Artemis Sunday, 16 January 2011 Valentin GUIGNON 24

  25. Annotation History Valentin GUIGNON

  26. Data Confidentiality GBrowse Access Restriction Valentin GUIGNON

  27. Data Confidentiality Access Restriction Administration Sunday, 16 January 2011 Valentin GUIGNON 27

  28. Sugarcane BAC Analysis Results • Some statistics… 17 scaffolds representing 1892242 bp 196 predicted genes Currently 284 genes with an average length of 2420 bp (36% of scaffolds) 8 predicted TE (transposable elements) Currently 132 TE with an average length of 3943 bp (28% of scaffolds) Valentin GUIGNON

  29. Other Sequence Analysis Results • Synteny Banana BAC / Rice Valentin GUIGNON

  30. Other Sequence Analysis Results Advanced Search Quick Search: « Hibernate Search » based Valentin GUIGNON

  31. Other Sequence Analysis Results • Genome Report System Valentin GUIGNON

  32. Other Sequence Analysis Results • Methabolic Pathway Valentin GUIGNON

  33. Sum up Sum up • Many annotation tools • High quality manual annotations • SouthGreen platform can help you See also… Presentations: W315, W107, W069, W152, W511, W327 and W585 Posters: P050, P800, P805 and P820 Valentin GUIGNON

  34. Thanks for your attention!

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