BIPAA resourcesfor genome annotation

bipaa@inra.fr http://bipaa.genouest.org

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Unpublished genomes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

bipaa@inra.fr for any question/feedback!