• 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 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

Cultures

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

EMBL

Sequence data bases: input

PICODIVenvironmentalcultures

Access database

Automatic query

Email 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

Webperiodic 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 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

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

Cultures Sequence

ProbesTaxonomy

Environment

Interacting data bases

It is our responsabilty to keep PICODIV databases updated

for the benefit of all