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

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Presentation transcript:

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

Valentin GUIGNON2 What is GNPAnnot 9 partners BIVI Spo GDEC >10 studied species

Sunday, 16 January 2011Valentin GUIGNON3 What is GNPAnnot 3 bioinformatics platform

Sunday, 16 January 2011Valentin GUIGNON4 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

Sunday, 16 January 2011Valentin GUIGNON5 GNPAnnot Concept

Sunday, 16 January 2011Valentin GUIGNON6 In House Annotation Pipeline Automatic genes structural & functional prediction Eugene FGenesHBlastxGenome ThreaderSpliceMachineEugene HMM DNA sequence (BAC) STRUCTURAL FUNCTIONAL blastp, tblastn, Interproscan, BBMH, Greenphyl

Sunday, 16 January 2011Valentin GUIGNON7 Repeats Automatic Annotation  Dawg Paws  Repet

Sunday, 16 January 2011Valentin GUIGNON8 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 2011Valentin GUIGNON9 Portal:

Sunday, 16 January 2011Valentin GUIGNON10 Portal:

Sunday, 16 January 2011Valentin GUIGNON11 Portal:

Sunday, 16 January 2011Valentin GUIGNON12 Portal:

Sunday, 16 January 2011Valentin GUIGNON13 Portal:

Sunday, 16 January 2011Valentin GUIGNON14 Portal:

Sunday, 16 January 2011Valentin GUIGNON15 Portal:

Sunday, 16 January 2011Valentin GUIGNON16 GBrowse

Sunday, 16 January 2011Valentin GUIGNON17 GBrowse

Sunday, 16 January 2011Valentin GUIGNON18 GBrowse

Sunday, 16 January 2011Valentin GUIGNON19 Artemis

Sunday, 16 January 2011Valentin GUIGNON20 Artemis

Sunday, 16 January 2011Valentin GUIGNON21 Artemis

Sunday, 16 January 2011Valentin GUIGNON22 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 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 2011Valentin GUIGNON23 Artemis

Sunday, 16 January 2011Valentin GUIGNON24 Artemis

Sunday, 16 January 2011Valentin GUIGNON25 Annotation History

Sunday, 16 January 2011Valentin GUIGNON26 Data Confidentiality GBrowse Access Restriction

Sunday, 16 January 2011Valentin GUIGNON27 Data Confidentiality Access Restriction Administration

Sunday, 16 January 2011Valentin GUIGNON28 Sugarcane BAC Analysis Results  Some statistics… 17 scaffolds representing 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)

Sunday, 16 January 2011Valentin GUIGNON29 Other Sequence Analysis Results  Synteny Banana BAC / Rice

Sunday, 16 January 2011Valentin GUIGNON30 Other Sequence Analysis Results Quick Search: « Hibernate Search » based Advanced Search

Sunday, 16 January 2011Valentin GUIGNON31 Other Sequence Analysis Results  Genome Report System

Sunday, 16 January 2011Valentin GUIGNON32 Other Sequence Analysis Results  Methabolic Pathway

Sunday, 16 January 2011Valentin GUIGNON33 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

Thanks for your attention!