The model-guided search for structurally-homologous RNAs is a non-trivial task, as it largely depends on the quality of the inferred structure model. When it comes to inferring RNA structures from chemical probing data, the challenges are numerous. Use of different chemical probes, or of different approaches for incorporating experimental reactivities as pseudo-free energy contributions can significantly affect the reliability of the inferred RNA structure model.
SHAPEwarp is a sequence-agnostic method for the identification of structurally-similar RNA elements in a database of chemical probing-derived reactivity profiles. The approach used by SHAPEwarp is inspired by the BLAST algorithm and builds on top of two widely used methods for similarity search in time series data: Mueen's Algorithm for Similarity Search (MASS) and dynamic time warping (DTW).
For support requests, please post your questions to: https://github.com/dincarnato/SHAPEwarp/issues
Edoardo Morandi (emorandi[at]rnaframework.com)
Danny Incarnato (dincarnato[at]rnaframework.com)
This program is free software, and can be redistribute and/or modified 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.
Please see http://www.gnu.org/licenses/ for more information.
- Linux system
- Rust and Cargo (Installation instructions: https://doc.rust-lang.org/cargo/getting-started/installation.html)
- RNA Framework v2.7.2 or higher (https://github.com/dincarnato/RNAFramework/)
- FFI::Platypus v1.56 or higher (https://metacpan.org/pod/FFI::Platypus)
- FFI::Platypus::Lang::Rust v0.09 or higher (https://metacpan.org/pod/FFI::Platypus::Lang::Rust)
Clone the SHAPEwarp git repository:
git clone https://github.com/dincarnato/SHAPEwarp
This will create a "SHAPEwarp" folder.
To compile the modules needed for kmer lookup issue:
cd SHAPEwarp perl Makefile.PL make make test
If the installation went fine, the expected output of the
make test command should look like the following:
"/usr/bin/perl" -MFFI::Build::MM=cmd -e fbx_build "/usr/bin/perl" -MFFI::Build::MM=cmd -e fbx_test PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/basic.t .. ok All tests successful. Files=1, Tests=1, 1 wallclock secs ( 0.03 usr 0.00 sys + 0.54 cusr 0.04 csys = 0.61 CPU) Result: PASS
SHAPEwarp builds on top of the RNA Framework. To use SHAPEwarp, the
lib/ folder of the RNA Framework must be added to the
PERL5LIB environment variable:
Testing the SHAPEwarp installation
To test SHAPEwarp on a small test dataset, issue the following command from within the SHAPEwarp install directory:
./SHAPEwarp -q t/query.txt -d t/ -o test_out -ow
The search will take <1 minute and the expected output should look like the following:
Query DB Qstart Qend Dstart Dend Qseed Dseed Score P-value E-value test 16S_Bsubtilis 7 170 916 1079 16-100 925-1009 173.76 4.83e-08 7.63e-06 ! test 16S_Bsubtilis 1 170 128 297 79-100 206-227 86.50 5.01e-04 0.08 ?