STAlign builds Structural Trees of 3D biomolecules (RNA, Proteins) and computes the Algebraic Structural Alignment (ASA) Distance.
Download the following files from folder download at
https://github.com/bdslab/STAlign/ - Direct link:
https://github.com/bdslab/STAlign/tree/master/download
STAlign.jar- executable jar of of the basic STAlign comparison toolSTAlignWorkbench.jar- executable jar of of the STAlign workbench comparatorSTAlignAux-vx.zip- auxiliary file of the last version of STAlign
and put them in any position of your drive.
Unzip the file STAlignAux-vx.zip with the facilities of your operating system.
The folder STAlignAux-<VersionNumber> is created containing the following files:
- STAlign-config.txt --- default STAlign configuration file
- STAlign-config-alternative.txt --- alternative STAlign configuration file
- examples --- folder containing sample input and output files
- INSTALL.md--- information on STAlign installation
- README.md --- STAlign description and usage information
- COPYING.txt --- copyright information
- LICENSE --- full GNU GPL Version 3 License
- CHANGELOG.txt --- information about the evolution of STAlign 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 https://www.oracle.com/technetwork/java/javase/downloads/index.html
- PDB format https://www.rcsb.org/
- Arc Annotated Sequence: includes the sequence (optional) and the bonds,
expressed as a list
(i_1,j_1);(i_2,j_2); ... ;(i_m,j_m)where each indexi_k, j_kbelongs to the interval[1,n]wherenis the length of the primary sequence andi_k < j_kfor allk.
> java -jar STAlign.jar -sc 1o0b -o 1o0b.txt
Produce file 1o0b.txt containing the linearised tree text of the structural tree
corresponding to the PDB molecule with code 1o0b.
> java -jar STAlign.jar -d -af examples/tRNA/1o0b.pdb examples/tRNA/1o0c.pdb
Print on the standard output the ASA distance between the two structural trees derived from the given PDB files.
See folder examples for some sample input files in both notations
coming from public databases or from the paper
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 STAlign-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 STAlignWorkbench.jar -f examples/tRNA
Processes all the files in folder tRNA. Each file is read as a
PDB file or Arc Annotated Sequence format. Comma-separated values files
STAlignProcessedStructures.csv and
STAlignComparisonResults.csv are created in the folder
"tRNA". The former contains the description of all the
biomolecules that were found and correctly processed. The latter contains,
for each pair of processed biomolecules, the ASA Distance between the two
correspondig structural trees and execution time information.
>java -jar STAlignWorkbench.jar -f examples/tRNA -o stucts.csv cmpr.csv -n my-config.txt
Processes all the files in folder tRNA as above but produce
the description of processed structures in file structs.csv and
comparison results in file cmpr.csv. Instead of using
STAling-config.txt default configuration file, use my-config.txt as
configuration file.
See folder examples for further examples of use.
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 STAlign comparator digit:
> java -jar STAlign.jar <options>
The following can be used:
-ac,--aligncode <input-pdb-code1 input-pdb-code2> Align two
given
structures by
PDB code
producing
alignment
tree and
distance
-af,--alignfile <input-file1 input-file2> Align two
given
structures by
PDB file
producing
alignment
tree and
distance
-am,--aligncustom <input-file1 input-file2> Align two
given
structures by
AAS file
producing
alignment
tree and
distance
-cm,--centerofmass Calculate the
distance
matrix with
center of
mass method
-d,--outdist Output only
distance, no
alignment
tree
-e,--showscores Show current
values of
edit scores
used for
alignment
-edc,--editdistancecode <input-pdb-code1 input-pdb-code2> Calculates
the edit
distance of
two given
structures by
PDB code
-edf,--editdistancefile <input-file1 input-file2> Calculates
the edit
distance of
two given
structures by
PDB file
-edm,--editdistancecustom <input-file1 input-file2> Calculates
the edit
distance of
two given
structures by
AAS file
-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
-p,--selectchains <chain-id> Calculate
only the
specific
chains of a
structure
-sc,--structcode <input-pdb-code> Produce the
structural
RNA/Protein
tree
corresponding
to the given
structure by
PDB code
-sf,--structfile <input-file> Produce the
structural
RNA/Protein
tree
corresponding
to the given
structure by
PDB file
-sm,--structcustom <input-file> Produce the
structural
RNA/Protein
tree
corresponding
to the AAS
file
-ssac,--ssaligncode <input-file1 input-file2> Align two
given
secondary
structures by
PDB code
producing
alignment
tree and
distance
-ssaf,--ssalignfile <input-file1 input-file2> Align two
given
secondary
structures by
PDB file
producing
alignment
tree and
distance
-ssc,--sscode <input-file> Produce the
secondary
structure
structural
RNA/Protein
tree
corresponding
to the given
structure by
PDB code
-ssf,--ssfile <input-file> Produce the
secondary
structure
structural
RNA/Protein
tree
corresponding
to the given
structure by
PDB file
-t,--threshold <threshold> Set a
threshold
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 STAlignWorkbench comparator digit:
> java -jar STAlignWorkbench.jar <options>
The following can be used:
-cm,--centerofmass Calculate the distance
matrix with center of
mass method
-e,--showscores Show current values of
edit scores used for
alignment
-edf,--editdistanceinput <input-folder> Process the files in the
given folder and
calculate edit distance
-edfm,--editdistanceinputcustom <input-folder> Process the bond files
in the given folder and
calculate edit distance
-f,--input <input-folder> Process the files in the
given folder
-fm,--inputcustom <input-folder> Process the bond 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
-t,--threshold <threshold> Set a threshold
STAling Copyright (C) 2022 BioShape and Data Science Lab at the University of Camerino, Italy
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 https://www.gnu.org/licenses/.
STAlign is developed and tested by:
- Filippo Lampa, University of Camerino
- Marco Serenelli, University of Camerino
- Luca Tesei, University of Camerino
STAlign is tested by:
- Michela Quadrini, University of Camerino
Please report any issue to [email protected] or to Luca Tesei, Polo Informatico, via Madonna delle Carceri 7, 62032 Camerino (MC) Italy.