JMGD: Java-based User Interface to the Microbial Genome Database
As the rate of progress in the determination of the whole genome sequencing of microbial organisms increases, we will need to have efficient, ready-to-use tools to publicize the data through WWW as soon as we finish the work. Java-based user interface to the microbial genome database (JMGD) can be used for almost any kind of circular microbial organisms. We use JMGD for the genome sequencing ofcyanobacterium we published recently. Java-based highlight-image techniques that were originally developed y Jim Graham(Sun Microsystem) are used in JMGD. JMGD includes all the Java source codes, perl scripts and the cgi scripts that are also used to blink the selected ORFs. The platform-independent aspect of Java makes it easily implemented in any machines used such as UNIX workstations, Macintosh or Windows computers.
JMGD has been developed under Sybase, but any other database management systems can be applied to without substantial modifications.
JMGD is available from:
The Haemophilus influenzae RD (TIGR)
The Mycoplasma genitalium RD (TIGR)
The Methanococcus jannaschii RD (TIGR)
0. Prerequisites: * software perl 5.003 or later JDK 1.02 (1.1 is not supported in the current release) sybperl 2.06 or later (http://www.perl.com/perl/CPAN/authors/id/MEWP) * OS Solaris 2.5 or later OSF1 3.2 or later * DBMS (Database Management System) SQL Server 10/11 or any other DBMSs can be used. If you have a Sybase SQL Server System 10/11, follow 1, 3(3-1), 5 if not, follow 1, 2, 3(3-2), 4, 5 1. set.data preparation Prepare set.data ( vars setting ) as instructed in data/README.data. 2. ORF, CLONE data preparation Prepare orf.data (putative ORF) clone.data (cosmid, phage etc. ) (optional) as instructed in data/README.data. 3. Run make_files INSTALL.csh, cgi/, html/ dirs and files are created. 3-1. run Make_Files.csh (sybase version) % Make_Files.csh 3-2. run Make_Files.csh (non-Sybase version) % Make_Files.csh -nosyb 4.Modify CGI programs ( for non-Sybase DBMS) Modify cgi programs to suit for your DBMS. 5.Install cgi scripts and html files. You should need to have a privilage to write to CGI and html dirs to run this script. % INSTALL.csh
Contact: Nobuyuki Miyajima