GNPAnnot Community Annotation System applied to sugarcane BAC clone sequences
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Transcript of GNPAnnot Community Annotation System applied to sugarcane BAC clone sequences
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GNPAnnot Community Annotation System applied to sugarcane BAC clone sequences
Valentin GUIGNONPAGSugarcane Genome Sequencing InitiativeSunday, 16 January 2011
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What is GNPAnnot
9 partners
BIVI
Spo
GDEC
>10 studied species
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What is GNPAnnot
3 bioinformatics platform
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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
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GNPAnnot Concept
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In House Annotation Pipeline
Automatic genes structural & functional prediction
Eugene
FGenesHBlastx Genome Threader
SpliceMachine Eugene HMM
DNA sequence (BAC)
STRUCTURAL
FUNCTIONALblastp, tblastn, Interproscan, BBMH, Greenphyl
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Repeats Automatic Annotation
Dawg Paws Repet
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About our Annotation Pipelines
Species-specific parameters Sugarcane trained on rice Already in use for full-genoms We can process your sequences
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Portal: http://www.gnpannot.org
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Portal: http://www.gnpannot.org
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Portal: http://www.gnpannot.org
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Portal: http://www.gnpannot.org
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Portal: http://www.gnpannot.org
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Portal: http://www.gnpannot.org
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Portal: http://www.gnpannot.org
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GBrowse
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GBrowse
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GBrowse
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Artemis
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Artemis
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Artemis
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ArtemisValidations:# 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).
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Artemis
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Artemis
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Annotation History
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Data Confidentiality
GBrowse Access Restriction
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Data Confidentiality
Access Restriction Administration
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Sugarcane BAC Analysis Results
Some statistics…17 scaffolds representing 1892242 bp196 predicted genesCurrently 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)
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Other Sequence Analysis Results
Synteny Banana BAC / Rice
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Other Sequence Analysis Results
Quick Search:« Hibernate Search » based
Advanced Search
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Other Sequence Analysis Results
Genome Report System
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Other Sequence Analysis Results
Methabolic Pathway
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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 W585Posters: P050, P800, P805 and P820
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Thanks for your attention!