Biology Reference
In-Depth Information
such as 3D-Coffee [
6
]. However, although such a technique
improves multiple sequence alignment, it cannot be applied to the
majority of protein sequences without known tertiary structures.
Aiming at overcoming such a problem, we have developed MSA-
Compro, a new multiple sequence alignment method, which effec-
tively utilizes predicted secondary structure, relative solvent
accessibility, and residue-residue contact map together with poste-
rior alignment probabilities produced by both pair hidden Markov
models and partition function as in MSAProbs [
4
]. Moreover,
applying predicted relative solvent accessibility and residue-residue
contact map to multiple sequence alignment is novel, although a
few attempts had been made to use predicted secondary structure
information [
7
-
12
].
Following the basic scheme in MSAProbs [
4
], MSACompro
has five main steps: (1) construct the pairwise posterior alignment
probability matrices based on both pair-HMM and partition func-
tion, utilizing the similarity in amino acids, secondary structure,
and relative solvent accessibility; (2) generate the pairwise distance
matrix from both the pairwise posterior probability matrices con-
structed in the first stage and the newly introduced pairwise contact
map similarity matrices; (3) build up a guide tree according to
pairwise distance matrix, and calculate sequence weights; (4)
adapt a weighting scheme to transform all the pairwise posterior
matrices; (5) perform a progressive alignment by computing the
profile-profile alignment from the probability matrices of all
sequence pairs, and then an iterative alignment to refine the results
from progressive alignment. Different from MSAProbs, our
method considers secondary structure and solvent accessibility
information in the calculation of the posterior residue-residue
alignment probabilities and computes the pairwise distance matrix
in light of predicted residue-residue contact information.
2 Materials
We released the latest version of the software MSACompro1.2.0 at
the MULTICOM toolbox Web site
http://sysbio.rnet.missouri.
edu/multicom_toolbox/tools.html
.
To install MSACompro,
users need to download Pspro2.0 package at the same Web site
first, and then install MSACompro according to the instruction in
the package.
The simplest way to use MSACompro1.2.0 is to go to ./script
directory of the software package and directly run the script auto_
run_msacompro.pl which automatically predicts secondary struc-
ture, solvent accessory and contact map information during the
alignment process. The standard command for auto_run_msacom-
pro.pl is:
./auto_run_msacompro.pl arg1 arg2 arg3
