MalDB

The creation of MalDB was supported with funds supplied by the Wellcome Trust.

Constuction of the MalDB began in December, 1996. It is based in ACeDB software, first developed by Richard Durbin (MRCLBB Cambridge, England) and Jean Thierry-Mieg (CNRS, Montpellier, France), as a readily accessible database for the species, A Caenorhabditis elegans.
The ACeDB program uses a structure of models (which can be different for each species) with cross referencing between DNA sequences, clones, strains, articles, and whatever other category that may be relevent to the genome project of the species. This allows for access to any data associated to any other data, whilst searching the database.
The ACeDB program also contains graphical displays of the chromosomes of the species, which may be searched for clones, sequences et al.
Software to enable the full use of ACeDB databases on the Internet is under construction; most ACeDB databases on the Internet, presently, being text oriented searches.
For further information about the ACeDB software, check the ACeDB documentation library at the Agricultural Genome Information Server (AGIS).

This software, used for MalDB, can be obtained from the National Center for Biotechnology Information (NCBI)'s FTP site.

MalDB Files

The above files are available at the MalDB ftp site. They can be transferred using ftp by
  1. ftp-ing to ftp.wehi.edu.au
  2. Logging in as "anonymous"
  3. going to the directory, pub/biology/who_dbase/MalDB .
    The conversion programs are in the subdirectory "ConversionPrograms" and the .ace files are in the subdirectory "acefiles".

To access the MalDB

Because a web based version of MalDB is not implemented, access to the database requires the following procedure;
  1. Install of the ACeDB software package: This software can be obtained at National Center for Biotechnology Information's FTP site. Download the INSTALL, NOTES, README files, and the binary file that is appropriate for your operating system (see NOTES). Read the beginning of the INSTALL script for installation instructions.
  2. Once the ACeDB software is installed in a directory, say acedb/, download and copy the above MalDB models and layout files to acedb/wspec/models.wrm and acedb/wspec/layout.wrm , respectively.
  3. Download the Acefiles.tar.Z to the acedb/ directory and uncompress it by typing uncompress acedb/Acefiles.tar.Z, and untar it, tar xvf acedb//Acefiles.tar. This will place all the MalDB .ace files in the acedb/rawdata directory.
  4. Now that all the .ace files are in the rawdata directory, they can be installed into the ACeDB database by typing textace from the acedb directory, and, then, from the textace application, typing the command, parse rawdata/file_name for each of the files that appear in the rawdata directory - apart from the Acefiles.tar file.
    Type quit to exit the textace application.
  5. The malaria genome data can now be accessed from the acedb/acedb or the acedb/textace applications.
As you can tell, this procedure requires some effort, and also takes up a lot of disk space, so it is advised that implementing MalDB be done only if one is intent on having an extensive malaria genome database in the ACeDB format.
If one is searching for a particular piece of data concerning the microbiology of malaria, nucleotide and protein sequence search engines can be found at http://www.wehi.edu.au/MalDB-www/genomeInfo/FTPaccess/ftp.html.

For technical questions concering the MalDB, e-mail robert.huestis@.med.monash.edu.au.

For questions concerning the malaria DNA, e-mail robert.huestis@med.monash.edu.au.

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