loopDloop in Java
an application for visualizing RNA secondary structure
loopDloop is a tool for drawing RNA secondary structures in
molecular biology. It will read files that include biosequence data
with base pairing information, and display views of the secondary
molecular structure. Options allow one to modify, adorn and edit
the structure. This program will not estimate base pairings needed
for secondary structure. For that, other software such as RNAFOLD,
MulFOLD, and multiple sequence alignment editors may be used.
NOTICE: This is a pre-beta version that is very preliminary and lacking
in several features.
This software is available at
loopDloop accepts data in three forms: CT (connect) file format used
by RNAFold, MulFOLD, GCG Fold and others; a file with interleaved
sequence and pairing character lines; or the format for Gary
Olsen's LOOPSOL program.
LoopDloop is now written as a Java application. This means that it
will run on most personal computers and workstations as a standard
program. The current release is lacking several features of prior
Macintosh releases, notably most of the editing features have not
yet been implemented.
One problem in using this program is that Java is still in preliminary
stages. You must fetch and install a Java runtime application and
library to use it. This can be obtained freely on the Internet. See for
To use, you will need these to fetch these files and folders
loopDloop.zip -- the program p-code
pix/ folder -- needed pictures
samples/ folder -- sample data files
doc/ folder -- documentation
and one of these depending on your computer system:
local/Macintosh/, local/MSWindows, or local/Unix folder
Developers will find the source code in the source/ folder.
These files are not needed for running the program. LoopDloop is
built on the beginnings of an application framework for Java, which
may make it easier to develop new applications.
by Don Gilbert
First java release: version 2.01, 8 December 96.
E-mail: software at bio.indiana.edu
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu