Micado


MICADO REFERENCE MANUAL

1  Getting Started with Micado

     1.1  Micado content
          1.1.1 Sequence data
	  1.1.2 Bacillus subtilis functional analysis data
     1.2  Access to the database
          1.2.1 Access to sequence data and their annotations
          1.2.2 Bacillus subtilis functional analysis project
          1.2.3  Explore the Micado Database
        1.3  How to contact Micado
     1.4  Releases
     1.5  History

2 Micado technical documentation

     2.1 Detailed description of Micado database structure
          2.1.1  General structure
          2.1.2  Tables and description
     2.2 Technical informations about interfaces
     2.3 Micado bibliography


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 :
http://www-mig.jouy.inra.fr/bdsi/Micado

	1.1  Micado content

		1.1.1  Sequence data

Micado provides easy access to GenBank and EMGlib sequences annotations.

			Sequences from GenBank
GenBank contains all public nucleic sequences data. Access and distribution
of these sequences are free. Information about GenBank are available at :
 ftp://ncbi.nlm.nih.gov/genbank/gbrel.txt.
Micado includes microbial primary sequences from GenBank. At this date, Micado contains
the 118777 microbial sequences of Release 126 of GenBank .
			Sequences from EMGLib (Enhanced Microbial Genomes Library)
This database 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.
Current release of Micado contains 55 complete genomes from EMGLib.
EMGLib sequences are available at the PBIL website at :
 http://pbil.univ-lyon1.fr/emglib/emglib.html.

			1.1.2  Bacillus subtilis functional analysis data

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
phenotypic tests.

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
database content.

	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 :

One to get all informations about a Genbank or Emglib 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 Emglib 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.


		1.2.2. Bacillus subtilis functional analysis project
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 :

growths curves in Rich and Minimal medium
reporter gene activity of strains
systematic determination of phenotype

Get more details on Protocols, phenotypes and laboratories involved in the BSFA project.


 
		1.2.3  Explore the Micado Database

  
  			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,
0 insertion'.


	1.3  How to contact Micado

At every Micado page, there is a link to contact the database in
case of problem or to comment. The mail addresses are :
chiapell@jouy.inra.fr or hoebeke@jouy.inra.fr

	1.4  Releases

	1.5  History

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
in preparation.



2  Micado Documentation


	  2.1  Detailed description of Micado database structure

The Relational DataBase Management System used is PostgreSQL 7.1.2

		2.1.1  General structure

			Sequence
	

	

			Mutant
	

	
   		2.1.2  Tables and description
              
                       Sequence

			Mutant

	2.2 Technical informations about interfaces

Programming and libraries :  Perl-CGI scripts which provide SQL access to the database.....
CGI, DBI/DBD, WML.

	 2.3 Micado bibliography

[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.
CABIOS, 1997.



[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
subtilis.
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.