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
AphidBaseLepidoDB
ParWaspDB
Today:
- Aphidius ervi- Aphis glycines- Daktulosphaira vitifoliae- Lysiphlebus fabarum
More to come, same environment
Information systemsMain website: http://bipaa.genouest.org
Published genomes
No account needed
Unpublished genomes
BIPAA account http://bipaa.genouest.org/account/
Per project credentials
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
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
Links to reports
Example search result: “gustatory”
Example polypeptide report
Example polypeptide report: Alignments
Links to JBrowse and Apollo
Example polypeptide report: Blast vs NR
Detailed alignment
Link to GenBank
Example polypeptide report: InterProScanLooks for known motifs in peptide sequences (gene families, catalytic sites, …)
Example polypeptide report: InterProScan
Links to InterPro pages
and/or external databases
Example polypeptide report: GO annotation
Links to terms description
Example mRNA report
Number of genes per GO-term
Global distribution
Download sequences
Query sequence
Reference sequences
Links to JBrowse, Apollo or gene reports
Download raw results
Download raw reference data
Fasta, GFF, functional annotation, ...
Common analysis tools (clustal, exonerate, RNASeq analysis, …)
Ready-to-use workflows
Reference data in the Data libraries
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
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
Getting in touchFeedback and suggestions highly appreciated!
We post news on http://bipaa.genouest.org
[email protected] for any question/feedback!