loopDloop in Java
an application for visualizing RNA secondary structure
version 2.07b, August 1997
loopDloop is a tool for drawing RNA secondary structures in molecular
biology. It reads files of biosequence data with base pairing
information, and displays graphic views of the secondary structure.
Options allow you to modify, adorn and edit the structure. Standard
application functions to save, print, edit and manage preferences are
included. This program will not produce base pairings needed for
secondary structure.
This software is available at
ftp://iubio.bio.indiana.edu/molbio/loopdloop/java/http://iubio.bio.indiana.edu/soft/molbio/loopdloop/java/
LoopDloop is now written as a Java application. This means that it
will run on most personal computers and workstations as a standard
program or application. The current release is lacking some features
of prior Macintosh releases.
Please read the installation instructions included in
loopdloop-doc.html with the software. The current release takes some
work to install, including perhaps a java runtime system for your
computer.
Java versions of other molecular biology applications built with
the same framework are or will soon be updated :
SeqPup - a biological sequence editor and analysis program
Phylodendron - a phylogenetic tree drawing application
FlyNapp - a FlyBase Drosophila database network application
The Java language has several important aspects and some current
drawbacks for biocomputing software. Please try some of these
programs and let me know if you think these are going in the
right direction.
Developers will find the source code all these applications in the
iubio:/molbio/java/source folders. The four current applications
share about 60% code. This framework may make a useful basis
for other biocomputing applications.
--
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu
