New information added:
- March 04 : New release available : 9.0
- May 03: New release available : 8.0
- July 02: For each new release, it is now possible to load only the new sequences from a smaller standalone ARB file called for release 7, SSURNA_PICODIV07.arb This file can be merged with your database (see below)
- June 02: A major change has been done for the ARB database. The ARB team has released a new version of the ARB database in June 02. This database takes advantage of the RDP and de Waechter alignments and therefore alignements are much more reliable. All sequences of the PICODIV project between releases 1 to 5 (20/02/02) have been moved to the new database. Then sequences sent to Roscoff since february 2002 have then been added. The latest release of the database is therefore version 6.0 and the details of the sequences added can be found below. You need to download both the database itself (SSURNA_PICODIV.arb) and the update file (SSURNA_PICODIV.a06). If you want to keep your old database you can merge the new sequences from release 6.0 using the procedure outlined in the link below, but you will want probably to do it the other way around, i.e. to move your sequences into the new database.
-
Conditions of use: All data remain the propriety of the group/individual that generate them. Therefore they cannot be used without his/her consent. All partners of the project have agreed that anyone who use someone else data should propose co-authorship to that person in resulting papers.
Distribution: All data from these databases are strictly for use within the PICODIV genome project and it is therefore forbidden to distribute them to third-parties.
Localisation: All databases are physically located on the Roscoff site.
Format: All major primary data bases are developped under Microsoft Access 97. This software has the advantage of being widely available as well as to be programmable fairly simply using Visual Basic. Sequence database are managed with the ARB software.
Update procedure: As soon as they become available, new data (sequences, probes etc...) are sent to Roscoff by email using special templates available through the Web (see below). These data are included in the corresponding master database, accessible also through the Web.
Download presentation about databases (june 2000).
Probe database
Primary database: Access format
Web database: Flat text file with PHP interface (RNA_probes.php3)
To submit new probes:
- download template file: RNA_probes_template.xls
- Fill in file without adding or removing any column
- email file to Daniel Vaulot
Taxonomy database
How to use the database
- Download the file Phytoplankton_species.zip
- Unzip the files keeping the directory structure as it is (select the correct WinZip option). The main Access file (Phytoplankton species.mdb) should be in a directory called \Cultures while all pictures are in a subdirectory called \Cultures\Phytoplankton images. If the directory structure is modified, then you will not be able to see any of the picture.
- Open Microsoft Access
- Go to the menu File/Open Database
- Select \Cultures\Phytoplankton species.mdb
- You cannot open the database by double cliclking from the file manager because the pictures will not show up
How to add and edit data
Warning: In Microsoft Access, any change made to a field is immediately taken into account and saved. There is no way to undelete changes once made. The only possibility is to keep always a replica of the database with a different name that can be reloaded in case of problem.
Pictures: Scan pictures at 75 or 100 dpi resolution. Using Photoshop or a similar programm create a compound image regrouping the key features of the species of interest (drawing, light microscope, whole mount, section). Keep the compound image small enogu that it can fit on a screen. Add scale on each part of the figure and label the scale directly on the picture. Save as JPEG file at x10 compression. The name of the file should be as follows: Genus_Species.jpg and the file should reside in the directory \Cultures\Phytoplankton images.
Fields: Species number is an automatic field that gets incremented everytime a new species is added. Date entered is automatically field with the current date for any new species added to the database.Some fields such as Length min, max etc... can only accept numeric values.
Pigment data: To add pigment data, move to the subform at the bottom of the species form. Enter first the species number for which you have pigment data and then check the different pigments present.
Remarks
The taxonomy database is not restricted to the sole picoplanktonic species. In particular, species from some of the major picoplankton classes (Prymnesiophytes, Prasinophytes, Pelagophytes) have been added and we will try to be as complete as possible.
Culture database
How to use the database
- Download the file RCC_catalog.zip
- Unzip the files.
- Double click on file Cultures de Roscoff.mdb from FileManager
Coastal sites (only Roscoff site at present)
Content
- Roscoff site
- Samples taken
- Hydrology (temp, sal, nutrients, chlorophyll, diatoms)
- Pigments
- Enrichment cultures
How to use the database
- Download the file Coastal_sites.zip
- Unzip the files.
- Roscoff site: Double click on file English Channel.mdb from FileManager
Sequence databases
Update history
As a general rule, only full length sequences from EMBL have been added to the database. In special cases, e.g. for plastid SSU sequences or some environmental sequences, partial sequences have been added.
|
Release
|
|
Sequences added
|
Eukaryote
|
|
| |
|
|
nucleus
|
mito
|
plastid
|
nucleo
morph
|
Synechococcus
Prochlorococcus
|
|
| .09 |
7/03/04 |
EMBL sequences
- Environmental Bay of Fundi
- Environmental Station Jericho
- Haptophyta
- Rhodophyta
PICODIV
- PROSOPE cruise DGGE et TTGE (D. Marie)
- Arabian Sea cultures (plastids, N. Fuller)
|
270 |
|
20 |
|
|
|
| .08 |
9/05/03
|
EMBL sequences:
- Loboesea
- Prasinophyceae Zingone
- Two environmental sets from Stoeck et al
- Stramenopiles Massana et al.
- Full sequences from Roscoff, Blanes Helgoland
- Cyanobacteria sequences
- Clones and DGGE from Blanes experiments (Laure)
- DGGE Vietnam (Laure)
PICODIV Cultures
- RCC (partial and full)
- Helgoland (SSCP)
- 16S Plastid sequences
|
558
(tree) |
|
60
(tree) |
|
45
(tree) |
8 |
| .07 |
26/07/02
|
EMBL sequences:
- Pinguiophyceae
- Dinophyceae
- Cryptophyceae
- Plastid sequence
- more...
|
198 |
|
18 |
|
9 |
|
| .06 |
17/06/02
|
EMBL sequences from clone libraries:
- Sogin: deep sea sediments (PNAS)
- Pace: marine sediments (PNAS)
- Amaral Rio Tinto (Nature)
PICODIV clone libraries
- Full sequences from Roscoff
- Blanes BL010320
PICODIV Cultures
- RCC (partial and full length)
- Bremerhaven SSCP (Klaus)
- Pirsonia from Klaus and Stefanie Kuhn
- Blanes (Laure)
|
695
(tree) |
|
|
|
|
|
|
.05
|
|
EMBL update: Euk (in particular Rhodophyta), Syn, Proc
Euk Clone libraries:
- Blanes BL000921 (corrected) and BL010625
- Assignement of Roscoff library sequences corrected
PICODIV Cultures
- RCC (partial and full length)
- Blanes (partial)
|
565
|
|
28
|
4
(leuco-plast)
|
5
|
|
|
.04
|
|
Euk Clone libraries:
- Roscoff July 01
- Public data from Lopez-Garcia et al 2001
PICODIV Cultures
|
124
|
|
|
|
|
|
|
|
|
PICODIV Euk Clone libraries:
- Roscoff Dec 00, April and May 01
- Helgoland Dec 00 Feb 01
- Blanes Sept, Dec
PICODIV Cultures
- RCC
- Synechococcus strains
PICODIV 16S Clone libraries:
- PROSOPE DYF and MIO
- Helgoland August
- Blanes Sept
|
|
|
|
|
|
|
|
|
|
EMBL update: Euk, Syn, Proc
PICODIV Euk Clone libraries:
- Roscoff Juin, Sept
- Helgoland Oct
- Orkney April
- Antarctic; North Atlantic and Mediterranean Sea
PICODIV 16S Clone libraries:
- PROSOPE DYF and MIO
- Helgoland August
|
378
|
|
12
|
5
|
87
|
8
|
|
|
|
EMBL update: Euk, Syn, Proc
PICODIV Euk Clone libraries (partial sequences):
- Roscoff April
- Helgoland March, April, August
|
309
|
|
29
|
6
|
1
|
|
|
.arb
|
|
EMBL Euk, Syn, Proc
OLIPAC unpublished
Euk Roscoff unpublished
|
714
|
4
|
26
|
7
|
52
|
|
Critical information (all must read)
Aligned sequences: main database (ARB format)
This database is based upon the ARB database available from the ARB site in Bremen. We are now using the June 2002 version.
The PICODIV ARB file is named SSURNA_PICODIV.arb. It is periodically updated with both public sequences and sequences from the PICODIV project. New sequences are aligned to the closest relative found by the PT-SERVER function and then added to partial parsimony trees using the "Quick add to tree" ARB function. If you are interested, you can find below the detailed procedure for updating the database.
In order to implement the database on your computer, you need to:
- Download the full database: SSURNA_PICODIV.arb if you do not have it already on your computer
- Erase or move to a backup directory your own latest save of the database ( (e.g. SSURNA_PICODIV.a82)
- Download the latest save of the database SSURNA_PICODIV.axx (e.g. a01, a02, a03 etc...).
- If you want to merge the new sequences in your existing database you can download only the new sequences in file SSURNA_PICODIVxx.arb (e.g. PICODIV07 etc...)
- Update your SSU_RNA PT-server (note: use a different sever for alignement e.g. SSU-RNA_align that is only updated once with the original database downloaded from the ARB web site)
- Other things to download:
- ebi.ift : slightly modified filter for EMBL sequences allowing the get the FT /clone field. Place the filter in /usr/arb/lib/Import
- PICODIV.mask: a specially designed mask to view sequences and update database information. Place this in directory /usr/arb/lib/inputMasks
How to add your own fasta sequences to your ARB database
- Move all sequence files to Linux station into your own directory
- All sequences must be in FASTA format with a clear identifier on the first line.
- Import sequences into your own arb file SSURNA_MyName.arb using the import filter fasta.ift
- Modify the following ARB fields immediately to be able to find the sequences easily:
- full name: add any precision here that may help qualify the sequence
- author: put your name here
- aligned: Indicates the date and the person who has performed the alignment.
Format is: "initials of aligner_DDMMYY" e.g. "DM_200503". If alignement is uncertain, add "redo".
- nuc: use the function provided by ARB to compute number of nucleotides
- Go to Sequence Editor
- Change all T to U (if not the automatic align function will not find the correct relative)
- Align using closest neighbour from PT-server SSU_rRNA_align
- Verify extremities of sequences which are often poorly aligned. Correct by hand
- Update the eukaryotic tree
- Filter: Do not use E.coli as a filter when adding sequences to trees:
- For individual sequences use closest neighbour
- For eukaryotic sequences use filter Stramenopiles
- Spot potential problems, re-align problematic sequences to nearest neighbor, remove from tree and re add to tree
- When sequences are clean reexport them to FASTA format using the full name as identifier and send the file to Daniel
How to update your own database without overwriting sequences that you have re-aligned
- Let us assume that you already downloaded version a03, have done some realignment in your local file and want to update to include the new sequences in .a04.
- Rename you own database to a new name renaming both the main file and the latest save you did. For example if you are now up to save 21:
- SSURNA_PICODIV.arb ---> SSURNA_Laure.arb
- SSURNA_PICODIV.a21 ---> SSURNA_Laure.a21
- Download the latest ARB datafiles both the main database and the latest save called in this case:
- SSURNA_PICODIV.arb
- SSURNA_PICODIV.a07
- Or you can also download an ARB file containing only the latest update
- You want now to merge the new sequences into your own database making sure that you preserve the alignment and the fields. To do this:
- Start ARB
- In first window, select Merge two ARB Databases
- Select SSURNA_PICODIV.arb or SSURNA_PICODIV07.arb as DB I and SSURNA_Laure.arb as DB II
- Select Transfer species item
- Select species in DB I the new species you want to transfer.
For exemple if you set
- Search field: PICODIV_release
- Search string: 7.
- This will select only species that have been added in the latest release a07.
- Here there are two cases
- Case 1 - If your ARB database (SSURNA_Laure.arb)is based on the latest ARB alignement from June 2002 (now the default alignement for PICODIV). In this case, the alignements of the two databases are identifical
- Unselect 'Preserve alignement'
How to submit sequences
All sequences must be submitted as FASTA files.
- The first line contains the identifier for the sequence, for exemple the clone library name followed by the clone number
e.g. >HE000420.015
corresponds partial sequence of Helgoland clone #15 from library of 20 april 2000
- Next lines contains the sequence itself
Other information (experts only)
ARB database structure
Trees
Three subtrees have been extracted from the general tree (tree_tre_1000_may02) and new sequences added to them (this is much faster):
|
Tree name
|
Method
of addition
|
Sequences |
Type of sequences added
|
|
|
Parsimony
|
> 5 000
|
nuclear: mostly lower eukaryotes
|
- tree_PICODIV_cyano_plastid
|
Parsimony
|
> 500 |
cyanobacteria and plastids
|
|
|
Parsimony
|
> 20 000 |
mito, bacteria
|
ARB database fields
- name: generated by ARB (do not change)
- acc: accession number from EMBL server
- full_name: Genus species strain or env.part.Clone_library.Clone_number
- ali_18S/data: Sequence data
- db_name: (same as full_name)
- id: (same as name)
- tax: Phylum; Division; Class; Order; Family
- The following fields have been updated for all PICODIV sequences, they allow quick search and query
- phylum: e.g. Alveolates, Chlorophyta, Stramenopiles
- class: e.g. Prasinophyceae, Chrysophyceae
- order: e.g. Mamiellales
- genus: e.g. Ostreococcus
- species: e.g. tauri
- strain: for cultures, name of the culture
- clone: for environmental samples, put the full clone designation eg. Clone_library.Clone_number
- aligned: Indicates the date and the person who has performed the alignment.
Format is: "initials of aligner_DDMMYY" e.g. "DV_200500". If alignement is uncertain, add "redo"
- authors: For unpublished sequences, indicate who has obtained the sequences
- nuc: Number of nucleotides in sequence (allows to identify quickly partial sequences)
- lab: can be used to identify laboratory that has obtained sequences
- pub: y if public, n for unpublished and PICODIV if generated by PICODIV program
- primer: contains information about primer/probe matching the sequence
Please note that some of the sequences (Accession number ZZ....) are still unpublished and were acquired prior to the PICODIV project. Therefore, they cannot be used freely.
PT-Server
PT-server are critical elements of ARB they allow alignement of novel sequences, finding closest relatives as well as designing and checking novel probes. We are currently using two PT-Server for the SSURNA_PICODIV database (to set PT-Server you need to modify (as user root) the end of the text file /usr/arb//lib/arb_tcp.dat.
- SSU_rRNA_PICODIV: This PT server is used for all function except alignement. It is updated with all the available sequences.
- SSU_rRNA_align: This PT server is used only for alignement. It has been created from the original ARB database of June 2002. It is NOT updated with the novel environmental sequences so that the original alignement is not polluted by misaligned novel sequences.
Sequence inventory (Access format)
This database contains all the rRNA sequences available for the lower eukaryotes as well as PICODIV sequences as they become available. The Access format allows easy manipulation, selection and formatting of the data.
How to add new sequences to the database (Administrator)
Note: The following is only for the person who maintains the database (Daniel for the time being). Other need not worry about this
Query of EMBL server to get recently released public sequences
- Query novel sequences from EMBL SRS server using a query of the type:
[libs={embl emblnew}-Organism:Acanthar*|Alveolata*|Chlorophyt*|Chlorara*|Choanoflag*|Cryptophy*|Glaucocyst*|Haptophy* |Kinetoplastida*|Rhizopoda*|Stramenopi*|Prochlorococcus|Synechococcus] & (([libs-FtKey: rRNA*])>parent)& [libs-LastUpdated# 21-Jul-2000:]
- Save result as full sequence in binary EMBL format
- Open the result file using the TextPad editor and re-save it in PC format (critical) because Access will not read UNIX formattted files.
Update of RNA algae.mdb
- Load Access database RNA algae.mdb
- Follow steps outlined in main menu of RNA algae Access database
- Import sequence as fasta file (text file in PC format, not UNIX) - Make sure that the Date and PICODIV release number are OK.
- Update all necessary fields. In particular check the following fields for each new sequence:
- Molecule: SSU, LSU etc...
- Encoded: nucleus, plastid, mitochondria etc...
- Partial: check box if the sequence is partial
- Environmental: check box if the sequence is from a clone library
- Strain, RCC, Clone number : for culture sequences
- Cruise, Station, Depth, Clone_library, Clone number : for clone library sequences
- Unpublished: true
- Method : clone library, DGGE, SSCP
- Author: put the name of the person who did or communicated the sequences
- Sequencing company : Qiagen, GenoMer etc....
|
- Export sequences in EMBL format. All the sequences exported into a single pseudo EMBL file. This file can now be imported into ARB (see below).
- EMBL sequences
- Import sequence as EMBL file (text file in PC format, not UNIX) - Make sure that the Date and PICODIV release number are OK.
- Update all necessary fields. In particular check the following fields for each new sequence:
- Molecule: SSU, LSU etc...
- Encoded: nucleus, plastid, mitochondria etc...
- Partial: check box if the sequence is partial
- Environmental: check box if the sequence is from a clone library
- Strain : for culture sequences
- Clone_library, Clone number : for clone library sequences
- Method : clone library, DGGE, SSCP
- Taxonomy (Phylum, class etc...): The program tries to fill these data automatically but sometimes this does not work that well
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Update SSURNA_PICODIV.arb
Last updated 08 March 2004
