@version 1.0
SERNAlign builds Structural Sequences starting from RNA secondary structures with arbitrary pseudoknots and computes SERNA Distance by aligning two Structural Sequences. Structural sequences are an abstraction of the arc diagram of a secondary structure in which the sequence of nucleotides is not considered and the topology of the arcs is represented by a numerical sequence. For each RNA secondary structure there is only ony corresponding structural sequence.
If you use SERNAlign please cite:
- Tesei, L., Levi, F., Quadrini, M., Merelli, E. "Alignment of RNA Secondary Structures with Arbitrary Pseudoknots using Structural Sequences". Submitted for publication. 2024
- 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.
Download the zip file of last version of SERNAlign from folder download at https://github.com/bdslab/sernalign/
Direct link: https://github.com/bdslab/sernalign/tree/master/download
and put it in any position of your drive.
Unzip the file with the facilities of your operating system. The folder
SERNAlign-<VersionNumber> is created containing the following files:
- SERNAlign.jar --- executable jar of the basic SERNAlign comparison
- SERNAlignWorkbench.jar --- executable jar for the SERNAlign workbench comparator
- examples --- folder containing sample input and output files
- INSTALL.txt --- information on SERNAlign installation
- README.md --- SERNAlign description and usage information
- COPYING.txt --- copyright information
- LICENSE --- full GNU GPL Version 3 License
- CHANGELOG.txt --- information about the evolution of SERNAlign 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 SERNAlign comparator digit:
> java -jar SERNAlign.jar <options>
The following can be used:
-a,--align <input-file1 input-file2> Align two given structures
producing an alignment and
distance
-d,--outdist Output only distance, no alignment
(works only with option -a)
-h,--help Show usage information
-i,--info Show license and other info
-o,--out <output-file> Output result on the given file
instead of standard output
-s,--struct <input-file> Produce the structural sequence
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) were placed. To launch the basic SERNAlignWorkbench comparator digit:
> java -jar SERNAlignWorkbench.jar <options>
The following can be used:
-f,--input <input-folder> Process the files in the given folder
-h,--help Show usage information
-i,--info Show license and other info
-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
Subfolder examples, distributed with SERNAlign, contains sample input files
from the paper: Tesei, L., Levi, F., Quadrini, M., Merelli, E. "Alignment of RNA Secondary
Structures with Arbitrary Pseudoknots using Structural Sequences". Submitted
for publication. 2024
> java -jar SERNAlign.jar -s examples/structS1.aas.txt
Print on the standard output the structural sequence corresponding
to the RNA secondary structure given in the Arc Annotated Sequence file
examples/structS1.aas.txt.
In this particular case, the output is
[ 1, 1, 5, 3 ]
> java -jar SERNAlign.jar -a examples/structS1.aas.txt examples/structS2.aas.txt -o examples/alignmentS1S2.txt
Write on the file examples/alignmentS1S2.txt the alignment and the SERNA
distance of the structural sequences corresponding to the RNA secondary
structures given in the Arc Annotated Sequence files examples/structS1.aas.txt and
examples/structS2.aas.txt.
In this particular case the file contains:
(1, 1)(1, 1)(5, 5)(-, 5)(3, 2)
Distance = 2
The sequence
(1, 1)(1, 1)(5, 5)(-, 5)(3, 2)
corresponds to the optimal alignmet
1 1 5 - 3
1 1 5 5 2
between the structural sequences 1 1 5 3 and 1 1 5 5 2 where the edit operations
are (1, 1) (match), (1, 1) (match), (5, 5) (match), (-, 5) (insertion)
and (3, 2) (mismatch/substitution).
The SERNA distance, i.e., the total cost of these edit operations is 0 (match) + 0 (match) + 0 (match) + 1 (insertion) + 1 (substitution) = 2
> java -jar SERNAlignWorkbench.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 "SERNAlignProcessedStructures.csv" and "SERNAlignComparisonResults.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 SERNA
Distance between the two structures and execution time information.
>java -jar SERNAlignWorkbench.jar -f TestWorkBench1 -o stucts.csv cmpr.csv
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.
See folder examples for some sample input folders containing structures
coming from public databases.
SERNAling Copyright (C) 2020 Luca Tesei, Francesca Levi, Michela Quadrini, 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.