PICODIV will amass large amount of data –cultures –sequences –environmental data Databases –keep track of data produced –verify the data –avoid errors.

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Presentation transcript:

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

Databases Taxonomy Cultures SSU rRNA sequences Probes Environmental data Other ? –Pigments –TEM pictures

Web site

Web data interface

Taxonomy

Taxonomy: pigments

Cultures: RCC catalog

Cultures: additional information PictureSpectrePigments Flow cytometry, RFLP

Cultures Starter cutures --> Environmental database Unialgal --> RCC catalog (not released)

EMBL Sequence data bases: input PICODIV environmental cultures Access database Automatic query as fasta file SSU vs LSU Full length ? Taxonomy ? VB program

Filtre

ARB aligned - phylogeny (trees) - probe design Sequence data bases: output Raw sequences - BLAST Access database Full sequences All sequences Web periodic update

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

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 nameMethodSequencesType of sequences added tree_all_dec98 Parsimony13804mito tree_euk_algae Parsimony1695nuclear: only lower eukaryotes tree_cyano_plastid Parsimony341cyanobacteria and plastids ARB trees

Probe database

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

CulturesSequence ProbesTaxonomy Environment Interacting data bases

It is our responsabilty to keep PICODIV databases updated for the benefit of all

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