ConStruct is an RNA alignment editor and consensus structure
prediction tool. It combines multiple sequence alignment,
thermodynamic structure prediction and statistics in a
semiautomatical fashion. Its sophisticated GUI guides the user
through correcting an initial sequence alignment with respect to a
consensus structure.
Its built-in
structure prediction routines allow for:
Optimal secondary structure (Basepair Maximization; Nussinov
et al., 1978) as well as
Suboptimal secondary structures (Steger et al., 1984; Zuker,
1989) and also
Tertiary interactions
e.g. pseudoknots (Maximum Weighted Matching; Tabaska et al., 1998)
cs_fold (ConStruct RNAfold front-end) creates thermodynamic base
pairing matrices for each sequence
Gaps from the
alignment are inserted into the matrices
The Mutual Information Content/Score (MI) is computed as measure
for compensatory base pair mutations
ConStruct's GUI (cs_dp): The base pair matrices (step 2) are
superimposed and displayed in a consensus dotplot (upper right
triangle). The MI is displayed in the bottom left part. Futhermore
an alignment editor is displayed. Upon changes in the alignment,
the consensus dotplot is directly updated.
Consensus structure prediction is done by a weighted (and
filtered) linear combination of the thermodynamic consensus
dotplot and the MI. Predicted structure can be viewed and stored
in a variety of formats (Circles-plot, color-coded
alignment, interactive squiqqles-like plot, connect, RNAML etc.)
Generic INSTALL instruction are included in the package tarball.
You will have to make sure that the following packages are already
installed on your system:
Configure, compile and install (as root) the package
$ ./configure $ ./make # ./make install
In some cases you will need to point configure to your tclConfig.sh
and tkConfig.sh. For example, on a Debian box you would have to
use: $ ./configure --with-tcl=/usr/lib/tcl8.4/ --with-tk=/usr/lib/tk8.4/
Download the
Debian package (3.2.4)
(i386 only) and type # dpkg -i
construct*.deb
If you don't have RNAfold installed, you may also
want to use this Debian
package (i386 only).
The following error is known to occur on some SuSE und Fedora machines
when cs_dp is started:
"Error in startup script: can't find package drawstructcore"
In most cases this is caused by a wrongly namend library. The following
procedure fixes the problem:
Cd to your ConStruct/DrawStruct library path: cd $PREFIX/lib/construct/drawstruct
Create a link with the correct name to the library: ln -s libdrawstructcore libdrawstructcore.so
Recreate the Tcl-Index: tclsh mkIndex.tcl . (Note the trainling dot!)
Create a sequence alignment of your RNA sequences.
Load this alignment in cs_fold
Click
"Write Project File" (writes an ASCII-file for cs_dp),
"Fold" (calls RNAfold for each sequence)
and "Exit"
Load the created project file (<alignmentfilename>.proj) in cs_dp
You can move nucleotides by selecting them with your mouse and
(left or right) clicking on the arrow button. Try to move
helices (green diagonal) on top of each other. This way they are
building a consensus helix (red diagonal).
Adjust the calculation options (menu: "Calculation_Base") to your
needs. For tertiary structure predicion you will have to set
a reasonable high multiplier for the MI.
Consensus structure prediction routines are called through the
"Structure_Prediction" menu.
Please have a look at this short demonstration.
For some more details see the manual (manual.pdf)).
References
Lück, R., Steger, G. & Riesner, D. (1996)
Thermodynamic prediction of conserved secondary structure:
Application to RRE-element of HIV, tRNA-like element of CMV,
and mRNA of prion protein. J. Mol. Biol.258, 813-826.
Lück, R., Gräf, S. & Steger, G. (1999)
ConStruct: A tool for thermodynamic controlled prediction of
conserved secondary structure. Nucleic Acids Res.21, 4208-4217.
