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Introduction, presentation of the Southgreen platform. http://southgreen.cirad.fr/. Manuel Ruiz, Bioinformatics School, Campinas, Sao Paulo, Brazil, 21-26 november 2011. Montpellier. The impact of NGS. Today within labs, bioinformaticians can perform a comprehensive analysis of

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southgreen.cirad.fr/

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  1. Introduction, presentation of the Southgreen platform. http://southgreen.cirad.fr/ Manuel Ruiz, Bioinformatics School, Campinas, Sao Paulo, Brazil, 21-26 november 2011

  2. Montpellier

  3. The impact of NGS Today within labs, bioinformaticians can perform a comprehensive analysis of TranscriptomicsGenome resequencing Tomorrow:Sequencing of new genomesMetagenomics: ecosystemsAfter :Sequencing cell / cell...

  4. Schatz MC, Delcher AL, Salzberg SL: Assembly of large genomes using second-generation sequencing. Genome Res, 20(9):1165-1173.

  5. de novo assembling

  6. How to apply de Bruijn graphs to genome assembly, Phillip E C Compeau ,Pavel A Pevzner , Glenn Tesler • Nature Biotechnology, 29,, 987–991 (2011)

  7. Mapping Trapnell C, Salzberg SL: How to map billions of short reads onto genomes. Nat Biotechnol 2009, 27(5):455-457.

  8. Stein LD: The case for cloud computing in genome informatics. Genome Biol 2010, 11(5):207.

  9. Stein, L.D. (2008) Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges, Nat Rev Genet,

  10. “ in a decade the cyberinfrastructure will be an absolutely indispensable part of the biological researcher’s equipment” Stein, L.D. (2008) Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges, Nat Rev Genet, “biological researchers will need to become familiar with the basics of computer science,[…], and have the skills to put this information in a form that can be readily adapted and re‑used by others in the community. This will require changes in the way biology is taught at the undergraduate and graduate levels”

  11. “ in a decade the cyberinfrastructure will be an absolutely indispensable part of the biological researcher’s equipment” Stein, L.D. (2008) Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges, Nat Rev Genet, “biological researchers will need to become familiar with the basics of computer science,[…], and have the skills to put this information in a form that can be readily adapted and re‑used by others in the community. This will require changes in the way biology is taught at the undergraduate and graduate levels” http://bloggingforconservation.blogspot.com

  12. http://southgreen.cirad.fr

  13. Stéphanie Sidibe Bocs • Funded by the French National Research Agency ANR (2008-2010) • CIRAD, Bioversity & INRA • Community annotation system (CAS) of structural and functional annotation • Automatic predictions and manual curations of genes and transposable elements • Based on GMOD components

  14. Gaëtan Droc http://orygenesdb.cirad.fr/tools.html/

  15. 16 plant species • 13.000 gene families • 587.000 genes v2.0 Matthieu Conte Jean-François Dufayard Mathieu Rouard

  16. Xavier Argout Marilyne Summo

  17. SNIPlay A web-based tool for SNP and polymorphism analysis. From sequencing traces, alignment or allelic data given as input, it detects SNP and insertion/deletion events, and sends sequences and allelic data to an integrative pipeline (haplotype reconstruction, haplotype network, LD, diversity) Alexis Dereeper

  18. Strategy : comparative population genomics with transcriptomics data Available reference ? genome/transcriptome No Yes 454 sequencing Solexa sequencing Solexasequencing De novo reference assembly Mapping on reference Ortholog/paralogs assignation • Polymorphism database in adapted format • redundancy • open reading frame • CDS/UTR • Diversitystudy • Comparative domestication • Life history trait impact • Functionnalevolution • CROP Breeding • SNP database • functional annotation • selectionfootprint

  19. Thanks to Equipe Intégration Des Données, UMR AGAP

  20. Thank you

  21. After

  22. Analyse comparative des transcrits • Problématique: homologie entre les transcrits. • Objectif: distinguer les paralogies des autres types d'homologies (allélisme, polymorphisme...) • Analyse comparative après l'étape d'assemblage

  23. Analyse comparative des transcrits Démarche: Regroupement en clusters Alignementmultiple Analysephylogénétique Reconstruction phylogénétique Implémentation sous GALAXY

  24. Analyse comparative des transcrits Alignement multiple Divergence totale Phylogénie Paralogies Seuil de divergence

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