@version 1.0
ASPRAling builds Algebraic RNA Trees and Structural RNA Trees or calculate ASPRA Distance by aligning Structural RNA Trees of RNA secondary structures with arbitrary pseudoknots.
If you use ASPRAlign please cite use:
- Quadrini, M., Tesei, L., Merelli, E. An algebraic language for RNA pseudoknots comparison. BMC Bioinformatics 20 (Suppl 4), 161 (2019). https://doi.org/10.1186/s12859-019-2689-5
- Quadrini, M., Tesei, L., Merelli, E. ASPRAlign: a tool for the alignment of RNA secondary structures with arbitrary pseudoknots, Bioinformatics, Volume 36, Issue 11, June 2020, Pages 3578–3579, https://doi.org/10.1093/bioinformatics/btaa147
- Extended Dot-Bracket Notation. See https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/rna_structure_notations.html
- Extended Dot-Bracket Notation without sequence (only structure)
- 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. - Arc Annotated Sequence without sequence (only structure)
- BPSEQ format, with or without header information, see https://www.ibi.vu.nl/programs/k2nwww/static/data_formats.html
- CT format, with or without header information, see https://www.ibi.vu.nl/programs/k2nwww/static/data_formats.html
All lines starting with # are considered comments. File format is automatically detected from the text file, any extension is accepted.
- ASPRAlign.jar (basic comparator and tree builder) and
- ASPRAlignWorkbench.jar (workbench comparator)
> java -jar ASPRAlign.jar -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 20, Article number: 161 (2019).
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2689-5
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.
> 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. 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.
Download the zip file of last version of ASPRAlign from folder download at https://github.com/bdslab/aspralign/
Direct link: https://github.com/bdslab/aspralign/tree/master/download
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.md --- ASPRAlign description and usage information
- COPYING.txt --- copyright information
- LICENSE --- full GNU GPL Version 3 License
- CHANGELOG.txt --- information about the evolution of ASPRAlign versions
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
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 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
-s,--struct <input-file> Produce the structural RNA tree
corresponding to the given
structure
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 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
ASPRAling Copyright (C) 2020 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/.
Please report any issue to luca.tesei@unicam.it or to Luca Tesei, Polo Informatico, via Madonna delle Carceri 9, 62032 Camerino (MC) Italy.