RIsearch1 (tauso fork)

RIsearch1: RNA–RNA, RNA-DNA and DNA-DNA interaction prediction using a simplified nearest-neighbor energy model.

This fork carries RIsearch1 only. RIsearch2 and the siRNA off-target pipeline live upstream at RTH-tools/risearch; they were removed here because nothing downstream of this fork uses them. Their history is still in this repository if you need it.

Python package

A precompiled binary from this fork is published to PyPI as risearch-tauso, so RIsearch is a normal Python dependency for tauso and any other downstream tool:

pip install risearch-tauso

import risearch_tauso, subprocess
subprocess.run([risearch_tauso.executable_path(), "-q", "query.fa", "-t", "target.fa"])

Or as a CLI shim, which forwards all arguments straight to the bundled binary:

risearch-tauso -q query.fa -t target.fa
python -m risearch_tauso -q query.fa -t target.fa

The PyPI package is not canonical upstream RIsearch — it is the tauso-team fork. Use upstream if you want the unmodified tool.

Differences from upstream

Bugs fixed relative to upstream are recorded in BUGFIXES.md.

Building from source

Requires a C++17 compiler and CMake 3.20 or newer.

cmake -S RIsearch1 -B RIsearch1/build -DCMAKE_BUILD_TYPE=Release
cmake --build RIsearch1/build -j

That produces RIsearch1/bin/RIsearch and RIsearch1/bin/RIsearch.dbg, the second with the debug tracing compiled in. The wheel build runs the same CMake via setup.py.

Tests

./RIsearch1/build/tests/risearch1_tests

Unit tests for the nucleotide coding, the min/max helpers, the alignment symbols, the energy matrix and the FASTA reader, including death tests for the inputs that are refused; end-to-end tests that run main() in process with a constructed argv and assert on its output; and throughput benchmarks under Performance.*. Pass -DRISEARCH_BUILD_TESTS=OFF to skip googletest entirely, as the wheel build does.

Running

RIsearch -q query.fa -t target.fa

Both files may hold several sequences; RIsearch scans all against all. Single sequences can be given directly with -Q acgu -T acgu. See RIsearch1/Manual.pdf for the full option list.

Copyright

Copyright 2021 by the contributors; see RIsearch1/README.

RIsearch1 is released under the GNU General Public License version 3. This is free software: you can redistribute it and/or modify it under the terms of that licence, either version 3 or (at your option) any later version. You should have received a copy of the GNU General Public License along with RIsearch — see the file COPYING. If not, see http://www.gnu.org/licenses/.

This software 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.

Citation

If you use RIsearch in a publication, please cite:

RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model. Wenzel A, Akbasli E, Gorodkin J. Bioinformatics. 2012 Nov 1;28(21):2738-46.

Contact

For problems with this fork, open an issue here. For upstream RIsearch: software+crispron@rth.dk