Skip to content
Algebraic Structural Pseudoknot RNA Alignment
Java
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
.settings
bin
doc
download
examples
executable-jar
lib
src/it/unicam/cs/bdslab/aspralign
.DS_Store
.classpath
.project
ASPRAlign-config-alternative.txt
ASPRAlign-config.txt
COPYING.txt
INSTALL.txt
LICENSE
README.txt

README.txt

***************************************************************************
ASPRAlign - Algebraic Structural Pseudoknot RNA Alignment - version 0.91
***************************************************************************

ASPRAling version 0.91 builds Algebraic RNA Trees and Structural RNA Trees
or calculate ASPRA Distance by aligning Structural RNA Trees of RNA secondary 
structures with arbitrary pseudoknots.

Default input file format is Extended Dot-Bracket Notation. 
See https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/rna_structure_notations.html

An alternative input file format is Arc Annotated Sequence, similar to 
the Extended Dot-Bracket Notation format in which the weak bonds are 
expressed as a list 

(i_1,j_1);(i_2,j_2); ... ;(i_m,j_m) 

where each index i_k, j_k belongs to the interval [1,n] (n is the length
of the primary sequence) and i_k < j_k + 1 for all k.

ASPRAlign is distributed with two executable jar files: ASPRAlign.jar (basic 
comparator and tree builder) and ASPRAlignWorkbench.jar (workbench comparator)

*** ASPRAlign.jar usage examples: ***

>java -jar ASPRAlign.jar -r -g aas1.txt -l -o aas1.tex

Produce file aas1.tex containing the LaTeX code to draw the algebraic RNA
tree corresponding to the RNA secondary structure given in the Arc
Annotated Sequence file aas1.txt

>java -jar ASPRAlign.jar -a rna1.dbn.txt rna2.dbn.txt

Print on the standard output the linearised alignment tree of the two
structural RNA trees corresponding to the two RNA secondary structures
given in the Extended Dot-Bracket Notation files rna1.dbn.txt and
rna2.dbn.txt

See folder "examples" for some sample input files in both notations
coming from public databases or from the paper: Michela Quadrini, Luca 
Tesei, Emanuela Merelli "An Algebraic Language for RNA Pseudoknots 
Comparison", BMC Bioinformatics 2019 (To Appear).  

Default output format is a linearised tree description of the form 

("node-label", [list-of-children])

An alternative output format is LaTeX code that can be processed with 
LaTeX to produce a graphical representation of the tree in a pdf file.
LaTeX format should be used for relative small structures, otherwise
the pdf file may not be produced or may be not readable.  

Default output stream is Standard Output. Output can be sent to a file 
using option -o 

The costs for the basic operations of alignment are specified in the default
configuration file ASPRAlign-config.txt. The values can be changed directly 
in this file or by using a different configuration file specified with 
option -n. The default configuration file must reside in the same folder in 
which the command is launched, while the file specified with option -n 
can reside in any folder.

*** ASPRAlignWorkbench.jar usage examples: ***

>java -jar ASPRAlignWorkbench.jar -f TestWorkBench1

Processes all the files in folder "TestWorkBench1". Each file is read as
an RNA secondary structure with arbitrary pseudoknots in Extended
Dot-Bracket Notation. Comma-separated values files
"ASPRAlignProcessedStructures.csv" and "ASPRAlignComparisonResults.csv"
are created in the folder "TestWorkBench1". The former contains the
description of all the structures that were found and correctly processed.
The latter contains, for each pair of processed structures, the ASPRA
Distance between the two structures and execution time information.

java -jar ASPRAlignWorkbench.jar -f TestWorkBench1 -o stucts.csv
cmpr.csv -n my-config.txt

Processes all the files in folder "TestWorkBench1" as above but produce
the description of processed structures in file "structs.csv" and
comparison results in file "cmpr.csv". Instead of using
"ASPRAling-config.txt" default configuration file, use "my-config.txt" as
configuration file.

See folder "examples" for some sample input folders containing structures 
coming from public databases.

***************************************************************************
INSTALLATION
***************************************************************************

Download the zip file of last version of ASPRAlign from folder "download" at

https://github.com/bdslab/aspralign

and put it in any position of your drive. 

Unzip the file with the facilities of your operating system. The folder 
ASPRAlign-<VersionNumber> is created containing the following files:

- ASPRAlign.jar --- executable jar of the basic ASPRAlign comparison
- ASPRAlignWorkbench.jar --- executable jar for the ASPRAlign workbench comparator
- ASPRAlign-config.txt --- default ASPRAlign configuration file
- ASPRAlign-config-alternative.txt --- alternative ASPRAlign configuration file
- examples --- folder containing sample input and output files
- INSTALL.txt --- information on ASPRAlign installation
- README.txt --- ASPRAlign description and usage information
- COPYING.txt --- copyright information
- LICENSE --- full GNU GPL Version 3 License 

The executable jar files runs on every Linux, Windows and Mac OS platform
in which a Java SE Runtime Environment 8 is installed. 

For information and installing the Java Runtime Environment see
http://www.oracle.com/technetwork/java/javase/downloads/index.html

***************************************************************************
USE
***************************************************************************

*** Using ASPRAlign

Open a terminal window of your operating system and use the change directory 
(cd) command to move to a folder in which the executable jar(s) and the
configuration file(s) were placed. To launch the basic ASPRAlign comparator 
digit:

> java -jar ASPRAlign.jar <options>

The following <options> can be used:

 -a,--align <input-file1 input-file2>   Align two given structures
                                        producing alignment tree and
                                        distance
 -c,--chkpair                           Check the presence of only
                                        standard Watson-Crick and wobble
                                        base pairing (disabled by default)
 -d,--outdist                           Output only distance, no alignment
                                        tree (works only with option -a)
 -e,--showscores                        Show current values of edit scores
                                        used for alignment
 -g,--alg <input-file>                  Produce the algebraic RNA tree
                                        corresponding to the given
                                        structure
 -h,--help                              Show usage information
 -i,--info                              Show license and other info
 -l,--latexout                          Output in LaTeX format instead of
                                        linearised tree
 -n,--useconffile <conf-file>           Use the specified configuration
                                        file instead of the default one
 -o,--out <output-file>                 Output result on the given file
                                        instead of standard output
 -r,--aasinput                          Input Arc Annotated Sequence
                                        file(s) instead of Extended
                                        Dot-Bracket Notation file(s)
 -s,--struct <input-file>               Produce the structural RNA tree
                                        corresponding to the given
                                        structure


*** Using ASPRAlignWorkbench

Open a terminal window of your operating system and use the change directory 
(cd) command to move to a folder in which the executable jar(s) and the
configuration file(s) were placed. To launch the basic ASPRAlignWorkbench 
comparator digit:

>java -jar ASPRAlignWorkbench.jar <options>

The following <options> can be used:

 -c,--chkpair                   Check the presence of only standard
                                Watson-Crick and wobble base pairing
                                (disabled by default)
 -e,--showscores                Show current values of edit scores used
                                for alignment
 -f,--input <input-folder>      Process the files in the given folder
 -h,--help                      Show usage information
 -i,--info                      Show license and other info
 -n,--useconffile <conf-file>   Use the specified configuration file
                                instead of the default one
 -o,--output <file-1 file-2>    Output structure descriptions on file-1
                                and comparison results on file-2 instead
                                of generating the default ouput files
 -r,--aasinput                  Input Arc Annotated Sequence file(s)
                                instead of Extended Dot-Bracket Notation
                                file(s)

***************************************************************************
COPYRIGHT and LICENSE
***************************************************************************

ASPRAling Copyright (C) 2018 Michela Quadrini, Luca Tesei, Emanuela
Merelli - BioShape and Data Science Lab at the University of Camerino,
Italy - http://www.emanuelamerelli.eu/bigdata/

This program is free software: you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the Free
Software Foundation, either version 3 of the License, or any later
version.

This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
for more details.

You should have received a copy of the GNU General Public License along
with this program.  If not, see <http://www.gnu.org/licenses/>.

***************************************************************************
CONTACT INFORMATION
***************************************************************************

Please report any issue to luca.tesei@unicam.it or to Luca Tesei, Polo
Informatico, via Madonna delle Carceri 9, 62032 Camerino (MC) Italy.

You can’t perform that action at this time.