picodiv will amass large amount of data –cultures –sequences –environmental data databases...
DESCRIPTION
Web siteTRANSCRIPT
![Page 1: PICODIV will amass large amount of data –cultures –sequences –environmental data Databases –keep track of data produced –verify the data –avoid errors](https://reader036.vdocuments.site/reader036/viewer/2022062412/5a4d1b077f8b9ab059988a6f/html5/thumbnails/1.jpg)
• PICODIV will amass large amount of data– cultures– sequences– environmental data
• Databases– keep track of data produced– verify the data – avoid errors– make data quickly available to all
• EU requirement
PICODIV databases
![Page 2: PICODIV will amass large amount of data –cultures –sequences –environmental data Databases –keep track of data produced –verify the data –avoid errors](https://reader036.vdocuments.site/reader036/viewer/2022062412/5a4d1b077f8b9ab059988a6f/html5/thumbnails/2.jpg)
Databases• Taxonomy• Cultures• SSU rRNA sequences• Probes• Environmental data• Other ?
– Pigments– TEM pictures
![Page 3: PICODIV will amass large amount of data –cultures –sequences –environmental data Databases –keep track of data produced –verify the data –avoid errors](https://reader036.vdocuments.site/reader036/viewer/2022062412/5a4d1b077f8b9ab059988a6f/html5/thumbnails/3.jpg)
Web site
![Page 4: PICODIV will amass large amount of data –cultures –sequences –environmental data Databases –keep track of data produced –verify the data –avoid errors](https://reader036.vdocuments.site/reader036/viewer/2022062412/5a4d1b077f8b9ab059988a6f/html5/thumbnails/4.jpg)
Web data interface
![Page 5: PICODIV will amass large amount of data –cultures –sequences –environmental data Databases –keep track of data produced –verify the data –avoid errors](https://reader036.vdocuments.site/reader036/viewer/2022062412/5a4d1b077f8b9ab059988a6f/html5/thumbnails/5.jpg)
Taxonomy
![Page 6: PICODIV will amass large amount of data –cultures –sequences –environmental data Databases –keep track of data produced –verify the data –avoid errors](https://reader036.vdocuments.site/reader036/viewer/2022062412/5a4d1b077f8b9ab059988a6f/html5/thumbnails/6.jpg)
Taxonomy: pigments
![Page 7: PICODIV will amass large amount of data –cultures –sequences –environmental data Databases –keep track of data produced –verify the data –avoid errors](https://reader036.vdocuments.site/reader036/viewer/2022062412/5a4d1b077f8b9ab059988a6f/html5/thumbnails/7.jpg)
Cultures: RCC catalog
![Page 8: PICODIV will amass large amount of data –cultures –sequences –environmental data Databases –keep track of data produced –verify the data –avoid errors](https://reader036.vdocuments.site/reader036/viewer/2022062412/5a4d1b077f8b9ab059988a6f/html5/thumbnails/8.jpg)
Cultures: additional informationPicture
Synechococcus MAX 42
0
0.2
0.4
0.6
0.8
1
400 450 500 550Longueur d'onde
Spectre Pigments
• Flow cytometry, RFLP
![Page 9: PICODIV will amass large amount of data –cultures –sequences –environmental data Databases –keep track of data produced –verify the data –avoid errors](https://reader036.vdocuments.site/reader036/viewer/2022062412/5a4d1b077f8b9ab059988a6f/html5/thumbnails/9.jpg)
Cultures
• Starter cutures --> Environmental database• Unialgal --> RCC catalog (not released)
![Page 10: PICODIV will amass large amount of data –cultures –sequences –environmental data Databases –keep track of data produced –verify the data –avoid errors](https://reader036.vdocuments.site/reader036/viewer/2022062412/5a4d1b077f8b9ab059988a6f/html5/thumbnails/10.jpg)
EMBL
Sequence data bases: input
PICODIVenvironmentalcultures
Access database
Automatic query
Email as fasta file
• SSU vs LSU
• Full length ?
• Taxonomy ?
VB program
![Page 11: PICODIV will amass large amount of data –cultures –sequences –environmental data Databases –keep track of data produced –verify the data –avoid errors](https://reader036.vdocuments.site/reader036/viewer/2022062412/5a4d1b077f8b9ab059988a6f/html5/thumbnails/11.jpg)
![Page 12: PICODIV will amass large amount of data –cultures –sequences –environmental data Databases –keep track of data produced –verify the data –avoid errors](https://reader036.vdocuments.site/reader036/viewer/2022062412/5a4d1b077f8b9ab059988a6f/html5/thumbnails/12.jpg)
Filtre
![Page 13: PICODIV will amass large amount of data –cultures –sequences –environmental data Databases –keep track of data produced –verify the data –avoid errors](https://reader036.vdocuments.site/reader036/viewer/2022062412/5a4d1b077f8b9ab059988a6f/html5/thumbnails/13.jpg)
ARB aligned
- phylogeny (trees)- probe design
Sequence data bases: output
Raw sequences
- BLAST
Access database
Full sequences
All sequences
Webperiodic update
![Page 14: PICODIV will amass large amount of data –cultures –sequences –environmental data Databases –keep track of data produced –verify the data –avoid errors](https://reader036.vdocuments.site/reader036/viewer/2022062412/5a4d1b077f8b9ab059988a6f/html5/thumbnails/14.jpg)
• Import files under EMBL format
• Mark all new sequences aligned: date + person (e.g. 20-jun-2000 DV) pub: n or PICODIV author: e.g. K Valentin
• Fast align by finding the closest relative with the PT-server SSU_RNA
• Quick add marked species to existing tree (use a sub-tree rather than the full tree)
• If tree incorrect remove from tree and align again to closest relative (either known or from BLAST search)
• Save only changes (not whole database)
• Update PT-Server
ARB processing
![Page 15: PICODIV will amass large amount of data –cultures –sequences –environmental data Databases –keep track of data produced –verify the data –avoid errors](https://reader036.vdocuments.site/reader036/viewer/2022062412/5a4d1b077f8b9ab059988a6f/html5/thumbnails/15.jpg)
Novel sequences have not been added to the full tree (tree_all_dec98), except for mitochondrial sequences. Two subtrees have been extracted and new sequences added to them:
Tree name Method Sequences Type of sequences added
tree_all_dec98 Parsimony 13804 mito
tree_euk_algae Parsimony 1695 nuclear: only lower eukaryotes
tree_cyano_plastid Parsimony 341 cyanobacteria and plastids
ARB trees
![Page 16: PICODIV will amass large amount of data –cultures –sequences –environmental data Databases –keep track of data produced –verify the data –avoid errors](https://reader036.vdocuments.site/reader036/viewer/2022062412/5a4d1b077f8b9ab059988a6f/html5/thumbnails/16.jpg)
Probe database
![Page 17: PICODIV will amass large amount of data –cultures –sequences –environmental data Databases –keep track of data produced –verify the data –avoid errors](https://reader036.vdocuments.site/reader036/viewer/2022062412/5a4d1b077f8b9ab059988a6f/html5/thumbnails/17.jpg)
Environmental data bases• One per site
• Sampling code
• Hydrological and meteorological data
• Sampling information (volumes, protocols etc…)
• Culture isolation data
• Measurement data
• flow cytometry
• pigments
• TEM
• probes
![Page 18: PICODIV will amass large amount of data –cultures –sequences –environmental data Databases –keep track of data produced –verify the data –avoid errors](https://reader036.vdocuments.site/reader036/viewer/2022062412/5a4d1b077f8b9ab059988a6f/html5/thumbnails/18.jpg)
Cultures Sequence
ProbesTaxonomy
Environment
Interacting data bases
![Page 19: PICODIV will amass large amount of data –cultures –sequences –environmental data Databases –keep track of data produced –verify the data –avoid errors](https://reader036.vdocuments.site/reader036/viewer/2022062412/5a4d1b077f8b9ab059988a6f/html5/thumbnails/19.jpg)
It is our responsabilty to keep PICODIV databases updated
for the benefit of all