BIPAA resources for genome annotation · annotation Search for your favorite gene (e.g. gustatory...
Transcript of BIPAA resources for genome annotation · annotation Search for your favorite gene (e.g. gustatory...
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INRA platform in Rennes (French National Institute for Agricultural Research)
Three full-time engineers
- Anthony Bretaudeau- Fabrice Legeai- Stéphanie Robin
Supports (post)genomic projects on insects associated to agroecosystems
- Omics data analysis- Information systems
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AphidBaseLepidoDB
ParWaspDB
Today:
- Aphidius ervi- Aphis glycines- Daktulosphaira vitifoliae- Lysiphlebus fabarum
More to come, same environment
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Information systemsMain website: http://bipaa.genouest.org
Published genomes
No account needed
Unpublished genomes
BIPAA account http://bipaa.genouest.org/account/
Per project credentials
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Information systemFor each genome:
- Reference assembly- Reference structural annotation
- OGS = Official Gene Set- Automatic (with Maker)- Based on RNASeq, transcript/protein alignments from related species, …- Associated functional annotation (Blast vs NR, InterProScan, Blast2GO, …)
- Home page giving access to web services- Transcript/polypeptide reports (Tripal)- JBrowse- Apollo- Galaxy- Blast- Download page
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Released data: assembly, structural and functional
annotation
Search for your favorite gene
(e.g. gustatory receptor,
DV000053-RA, GO id, …)
Availables services for this genome
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Links to reports
Example search result: “gustatory”
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Example polypeptide report
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Example polypeptide report: Alignments
Links to JBrowse and Apollo
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Example polypeptide report: Blast vs NR
Detailed alignment
Link to GenBank
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Example polypeptide report: InterProScanLooks for known motifs in peptide sequences (gene families, catalytic sites, …)
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Example polypeptide report: InterProScan
Links to InterPro pages
and/or external databases
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Example polypeptide report: GO annotation
Links to terms description
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Example mRNA report
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Number of genes per GO-term
Global distribution
Download sequences
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Query sequence
Reference sequences
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Links to JBrowse, Apollo or gene reports
Download raw results
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Download raw reference data
Fasta, GFF, functional annotation, ...
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Common analysis tools (clustal, exonerate, RNASeq analysis, …)
Ready-to-use workflows
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Reference data in the Data libraries
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What’s next?More genomes!
More features!
- Orthology- Links from each gene to orthologs in other species (BIPAA-hosted, external, OrthoDB)- OrthoMCL/OrthoDB/...
- Expression tables- Synteny
More data! Send us new RNASeq or alignments data to ease annotation!
More user-friendliness! Working on improving the web UI
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What’s next?AskOmics
Web application for data integration and querying (RDF, SPARQL)
http://github.com/askomics/askomics
Hands-on workshop
10th Arthropod Genomics Symposium - Arthropod Bioinformatics Workshop
June 8th 2017
Eck Institute for Global Health
University of Notre Dame
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Getting in touchFeedback and suggestions highly appreciated!
We post news on http://bipaa.genouest.org
[email protected] for any question/feedback!