1 Getting Started with Micado
Micado (MICrobial Advanced Database Organization) is a relational database dedicated
to microbial genomes [Biaudet, 1997] and functional analysis of Bacillus subtilis [Samson, 2000].
The database is accessible on the web at the URL :
1.1 Micado content
1.1.1 Sequence data
Micado provides easy access to GenBank and NCBI sequences annotations.
1.1.2 Bacillus subtilis functional analysis data
- GenBank entries (primary data). Genbank contains all public nucleic sequences data. Access and distribution
of these sequences are free. Information about GenBank are available at :
Micado includes microbial primary sequences from GenBank.
- NCBI entries (completes genomes, checked annotation) contains all the complete genomes from prokaryotes (bacteria
and archea) in GenBank format [Perrière, 2000].
It also provides sequence annotations improved by the introduction of data on
codon usage, gene orientation on the chromosome and gene families.
NCBI sequences are available at :
The goal of functional genomics is to unravel the physiological functions of
genes. Bacillus subtilis genome contains 4100 protein-coding genes. Among
these genes, 1200 genes of unknown function have been chosen with the aim
to elucidate their function.
So these 1200 genes have been specifically and systematically disrupted
in a mutant strain of B. subtilis. These strains have been studied by an
european consortium of 17 laboratories. The physiological data tested are :
growth and gene reporter activity (betagalactosidase), RNAm transcripts and
All these data are linked, so it is possible to navigate between the different
parts of the database. There are many different possibilities to access to the
1.1.3 Bacillus subtilis genetic map data
This part contains genetic map data produced in 1993 for B. subtilis[Anagnos, 1993]. It describes gene names and synonyms, gene positions on the genetic map and associated bibliographic references.
1.2 Access to the database<
Information on sequences, genes and mutants is searched through hyperlinked
menu pages, composed of selectable lists and options, text input, and
graphical navigation on clickable images.
1.2.1 Access to sequence data and their annotation
Two forms are available from Micado main page :
1.2.2. Bacillus subtilis functional analysis project
- One to get all informations about a Genbank or NCBI complete genome access number
After this query, the web page contains three kinds of results :
the physical map of the sequence contained in the access number, sequence
extraction facilities for the considered acces number (DNA sequence,
locations...) and a table including all the features/qualifiers of the
considered access number.
- One to get all informations about a gene name in a species for which the complete genome is in the Micado database.
The results include all the Genbank or NCBI complete genome access number which cited the gene name in the qualifier 'gene'. If this query don't give any result, the search is performed on the qualifier 'note' but results are more approximate. Links to PubMed, Swiss-Prot are systematically included. Additionnal links to Subtilist, Jafan and the Functionnal Analysis Page of Micado are included only for Bacillus subtilis genes.
In this part information is accessible by gene name either in a form or via three list of genes (BSFA, JAFAN or essential genes).
You will find in this part three kinds of results :
Get more details on Protocols, phenotypes and laboratories involved in the BSFA project.
- growths curves in Rich and Minimal medium
- reporter gene activity of strains
- systematic determination of phenotype
1.2.3 Explore the Micado Database
1.3 How to contact Micado
- BLAST/FASTA against the Micado Database or one of the complete genomes
By this way, you can compare your own sequence to a set of Micado sequences
with three programs :Fasta, blast and psi-blast. Sequence may be protein
or DNA sequence.
- Search pattern in Micado sequences
The pattern matching software used in this section is Patscan [Dsouza, 1997].
Pattern in DNA or protein sequence may be searched in three kinds of Micado
sequences : a unique sequence, a set of sequences or in a complete genome. To
definite the pattern, see the link ``Look at the rules for pattern definition''.
Example : TATAA[1,0,0] means 'match TATAA allowing 1 mismatch, 0 deletion,
At every Micado page, there is a link to contact the database in
case of problem or to comment. The mail addresses are :
Helene.Chiapello @ jouy.inra.fr or Annie.Gendrault-Jacquemard @ jouy.inra.fr
Micado database was built in the ``Génétique Microbienne'' laboratory at INRA
(Jouy-en-Josas) to replace the first database MadBase [Biaudet, 1995], to
store the increasing number of data (thanks to genome sequencing projects,
their analysis and a new functional analysis program of unknown genes ),
to manage them and to allow their consultation.
- 1994-1999 : Micado creation from the work of Véronique
Biaudet-Brunaud who more particularly worked on Micado structure and
content [Biaudet-Brunaud, 1997]. The interface development was performed
by Franck Samson. This group was managed by Philippe Bessières.
- From February 2000 : Hélène Chiapello (structure,
content and interfaces) and Mark Hoebeke (graphical interfaces) take over
their activity, in the MIG laboratory, a new bioinformatic lab at INRA. Philippe
Bessières still managed this group. A new major release of Micado is
2 Micado technical Documentation
2.1 Database structure
The Relational DataBase Management System used is PostgreSQL 7.3.3.
2.1.1 Relationnal model
2.1.2 Tables and description
|Table name ||Field number|| Content |
|ACCESSIONS || 2 || Sequences with a changed accession number|
|ARTICLES || 7 || Bibliographic references of the Genbank entry|
|COMMENTS || 2 || Comments on accession numbers|
|COMPLETE_GENOMES || 3 || Description of complete genomes entries from NCBI|
|DNA_LOC || 5 || DNA sequence of each location site|
|DNA_SEQ || 2 || DNA sequence of each Genbank entry|
|FEATURES || 7 || Features description of GenBank/NCBI complete genome entries|
|KEYWORDS || 2 || Keywords used in GenBank sequences|
|LOCATIONS || 9 || Description of each location site of each feature|
|PROT_FEAT || 2 || Protein sequences issued from DNA sequences (CDS)|
|QUALIFIERS || 4 || Qualifiers describing feature properties|
|SEQUENCES || 17 || Main description of the Genbank entry|
2.2 Web interfaces
|Table name || Field number || Content|
|BSFA_ARTICLEMUTANT || 10 || Bibliographic references about
|BSFA_CHECKMETHOD || 14 || Description of controls|
|BSFA_GROWTHCURVE || 14 || Growth curve of strains and reporter gene activities|
|BSFA_INFOREGION || 4 || Informations (features) on a given bsfa region|
|BSFA_LABOPHENO || 3 || List of involved laboratories involved in a phenotype study|
|BSFA_LSLABO || 3 || List of all laboratories|
|BSFA_LSPHENO || 2 || List of phenotypes|
|BSFA_PROTOCOLCOLUMN || 5 || All column titles for results tables|
|BSFA_PROTOCOLCURVE || 11 || All values of curves results|
|BSFA_PROTOCOLDESC || 6 || List of protocols, used in functional analysis|
|BSFA_PROTOCOLTABLE || 7 || Results of experiences (without curve)|
|BSFA_REFART || 3 || Association table Articles/strainmutants|
|BSFA_REGIONS || 5 || Description of bsfa regions|
|BSFA_STRAINMUTANT || 21 || Description of mutant strains|
|BSSFA_STRAINPROTOCOL || 23 || Summary of protocol results for each gene|
All Web interfaces are Perl/CGI scripts. Used Perl libraries are CGI and DBI/DBD.
2.3 Micado bibliography
- [Anagnos, 1993]
Anagnostopoulos C., P. J. Piggot & J. A. Hoch (1993). The Genetic Map of Bacillus subtilis.
In : Sonenshein A. L., J. A. Hoch & R. Losick (eds.). Bacillus subtilis and other Gram-Positive Bacteria.
American Society for Microbiology, Washington, D.C.. 425-461.
- [Biaudet, 1995]
Véronique Biaudet, Franck Samson & Philippe Bessières.
MadBase : a Networked Relational Database for Microbial Genomes.
Second Meeting on the Interconnection of Molecular Biology Databases
Cambridge, United Kingdom - July 20-22, 1995.
- [Biaudet, 1997]
Véronique Biaudet, Franck Samson, Philippe Bessières.
Micado a network oriented database for microbial genomes.
- [Biaudet-Brunaud, 1997]
Thesis of Véronique Biaudet-Brunaud.
Développement d'une base de données de génomes microbiens, et étude
des séquences Chi recombinogènes.
Université Paris VI, 1997.
- [Dsouza, 1997]
Dsouza, M., Larsen, N., Overbeek, R.
Searching for patterns in genomic data.
Trends in genetics, 1997.
- [Hart, 1994]
Hart KW, Searls DB, Overton GC.
SORTEZ: a relational translator for NCBI's ASN.1 database.
Comput Appl Biosci, Jul 1994.
- [Kroeger, 1997]
Kroeger, M. and Wahl, R.
Compilation of DNA sequences of Escherichia coli K12; description of
the interactive databases ECD and ECDC (update 1996).
Nucleic Acids Research, 1997.
- [Kunst, 1997]
Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G,
Azevedo V, Bertero MG, Bessières P, Bolotin A, Borschert S, Borriss R,
Boursier L, Brans A, Braun M, Brignell SC, Bron S, Brouillet S,
Bruschi CV, Caldwell B, Capuano V, Carter NM, Choi SK, Codani JJ,
Connerton IF, Danchin A, et al.
The complete genome sequence of the gram-positive bacterium Bacillus
Nature, Nov 1997.
- [Moszer, 1995]
Moszer I, Glaser P, Danchin A.
SubtiList : a relational database for the Bacillus subtilis genome.
Microbiology, Feb 1995.
- [Perrière, 2000]
Perrière G, Bessières P, Labedan B.
EMGLib : The enhanced microbial genomes library (update 2000).
Nucleic acids res, Jan 2000.
- [Samson, 2000]
Franck Samson, Véronique Biaudet-Brunand, Shahinaz Gas,
Etienne Dervin, Gabriel Gallezot, Sandrine Duchet, Jean-Michel Batto,
S.Dusko Ehrlich and Philippe Bessières.
Micado, an Integrative Database Dedicated to the Functional Analysis
of Bacillus subtilis and Microbial Genomics.
Functional Analysis of Bacterial Genes, 2000.