Looking for Ecoli Genome database

Luc Simon lsimon at alnus.for.ulaval.ca
Fri Mar 25 14:02:03 EST 1994

In article <pagilbert-230394170011 at cube.bcm.ulaval.ca>,
pagilbert at cti.ulaval.ca (Philippe-Alexandre Gilbert) wrote:

> I'm looking for any informations which could permit me to find a kind of
> Ecoli Genome Database or Ecoli Map database. We would like to find where
> are located our sequence patterns on the Ecoli Genome . Is GCG able to do
> that kind of research ? Any idea ?

There is a database called COLIBRI which is available via anonymous FTP at

Here is their readme file:
Sun Jan 10 1993

-1- Presentation

Colibri is a Data Base dedicated to the analysis of the Escherichia coli
It was developped as a part of a thesis project (C. Medigue) through a 
collaboration between the Laboratoire de Regulation de l'Expression 
Genetique (CNRS- Inst. Pasteur) and the Atelier de BioInformatique 
(Inst. Curie). 

A complete description of the database and its organisation can be found in

  "Colibri : a functional database for the E. coli genome"
   C. Medigue, A. Viari, A. Henaut and A. Danchin
   Microbiological Review (Submitted) 
   (this reference will be updated as soon as possible) 

-2- System requirement

Colibri is a Macintosh application developped with the 4D database engine
(ACI). However, you do not need to have 4D running on your Mac since
includes a runtime of the engine. This runtime, however, will not let you 
add nor modify the records in the database. The application was designed
to let you consult and export information from the database in an easy way.

You need a Mac (any CPU) running MacOS 6.04 or later (including system 7),
with a 13 inch <at least> monitor.
Caution : Colibri cannot be launched on a 12 inch monitor (LC monitor) or 
          less (Mac Plus, Classic, or SE screens).
          Monochrome monitors are supported, although best results are 
          obtained with a color monitor in 256 colors mode.
The Colibri application needs 1.5 Mb of RAM. 
In order to install Colibri on your Mac, you need at least :

    ~ 2 Mb of free disk space for the application (version 2.0)
    ~ 14 Mb  of free disk space for the data  (data release 002)
   (+ an overhead of about 5 to 7 Mb for temporary files during

-3- Files

Note : If you are not familiar with ftp, please consult the README file at
       the ftp root directory (/pub) for general informations about file 
       formats and ftp transferts.

Colibri is composed of 2 Mac files : the application and the data file. 
Theses files are available on  radium.jussieu.fr, in 3 differents formats :
Note:  Some Colibri files have a big size and may take a couple of time
       to transfert. Use the files in the /pub/mac_samples to experiment
       with file transferts if you are not sure which format is the most
       convenient for you. (in case of doubt, use "binhexed" files)

a) binary files
    colibri_2.0.sea  (compressed application) (1 Mb)
    colibri_002.data.sea (compressed data)  (4 Mb)

b) binhexed files (a safe choice)
     colibri_2.0.sea.hqx  (binhexed compressed application) (1 Mb)
     colibri_002.data.sea.hqx (binhexed compressed data)  (5 Mb)

c) segmented files - for the data file only - (for transferts on floppies)
     colibri_002.data.sea.1.hqx   (binhexed compressed data - segment 1)
     colibri_002.data.sea.2.hqx   (binhexed compressed data - segment 2)
     colibri_002.data.sea.3.hqx   (binhexed compressed data - segment 3)
     colibri_002.data.sea.4.hqx   (binhexed compressed data - segment 4)
     colibri_002.data.sea.5.hqx   (binhexed compressed data - segment 5)

Also, get the "README.install" (ascii) file which explains how to install
and launch the database on your Mac form the compressed files.

-a- binary files :
      Shoud be transfered in ftp <binary> mode. 
      When transfering them onto your Mac (ie either directly from radium 
       or through an intermediate unix host), turn on the "MacBinary"
       of your communication software (if this feature exists).
-b- binhexed (ascii) files :
      Transfert in ftp ascii mode. This is a safe (but a little bit longer)
      way to get the files.

-c- segmented files (for the data file only).
       This format is intended for people whose Mac is not directly
       on a network. The data file has been segmented to fit on 5 (high
       floppy disks. Most Unix workstation have 3.5' floppy drive able to
       read/write in DOS (PC) format. So if you have a high density floppy 
       drive on your Mac it becomes possible to transfert files via the 
       standard Apple File Exchange program (use the binhexed ascii files 
       (.hqx) and the "Straight Copy" text mode in Apple file Exchange). 
       However you should contact your Unix system manager in order to
       the DOS diskets on the workstation. Also, you may need to change the
       file names (since their names may be too long for DOS...)
       An alternative is to use the Suntar utility (see in the
       directory) which enable to read Sun diskets in tar format on a Mac.
       In both case, ask help to your unix system manager.
       Note : the segmented files are located in the "segmented"
-d- if all else failed... 
       Send 6  3.5' high density (1.4 Mb) floppy disks or (better) a 40 Mb
       Syquest cartridge to :

              Secretariat de Mr A. Danchin
              Laboratoire de Regulation de l'Expression Genetique
              Institut Pasteur
              28, rue du docteur Roux, 75724 Paris C/dex 15
-4- Installation

Once you have got the files on your Mac,  please consult the 
"README.install" file.

-5- Data releases and Updates

The "NEWS" file, give an historical description of the colibri files. 
Get and consult this file from time to time. 
When a  new release of the database appear, you need to reload the whole
datafile (not the application unless there is an application upgrade too).
The possibility of "differential" files is currently beeing studied.

In case of difficulties, please do not hesitate to contact :
               bunny at radium.jussieu.fr

Luc Simon
Universite Laval
Sainte-Foy, Que

lsimon at rsvs.ulaval.ca

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