https://github.com/seqan/mars
Motif-based aligned RNA searcher
https://github.com/seqan/mars
descriptors motif rna-structure
Last synced: 3 months ago
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Motif-based aligned RNA searcher
- Host: GitHub
- URL: https://github.com/seqan/mars
- Owner: seqan
- License: other
- Created: 2020-06-22T12:13:29.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2022-08-11T09:59:35.000Z (almost 3 years ago)
- Last Synced: 2025-01-13T12:23:42.496Z (4 months ago)
- Topics: descriptors, motif, rna-structure
- Language: C++
- Homepage:
- Size: 7.71 MB
- Stars: 0
- Watchers: 8
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
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README
# MaRs: Motif-based aligned RNA searcher
[](https://github.com/seqan/mars/actions?query=branch%3Amaster+workflow%3A%22Mars%20CI%22)
[](https://github.com/seqan/mars/blob/master/LICENSE.md)
[](https://github.com/seqan/mars/blob/master/README.md)
Mars is a tool that reads a structural multiple RNA alignment (e.g. from LaRA) and derives fuzzy stem loop descriptors
from it. These descriptors are then subject to a search in a genomic database and Mars returns the hits where the
RNA structure is found, accompanied with a quality value for each hit.
## Download instructions
Clone the repository and use the *-\-recurse-submodules* option for downloading SeqAn as submodule.
```commandline
git clone --recurse-submodules https://github.com/seqan/mars.git
```
Alternatively, you can download a zip package of the repository via the green button at the top of the github page.
If you do so, please unzip the file into a new subdirectory named *mars* and download the dependencies separately.
## Requirements
* platforms: Linux, MacOS
* compiler: gcc ≥ 7
* cmake ≥ 3.8
Mars is dependent on the following libraries:
* [SeqAn 3.0.2](https://github.com/seqan/seqan3.git)
* [IPknot](http://rtips.dna.bio.keio.ac.jp/ipknot) (shipped in the _lib_ directory) with the following dependencies:
* [ViennaRNA 2](https://www.tbi.univie.ac.at/RNA)
* [GLPK (GNU Linear Programming Kit) 4](https://www.gnu.org/software/glpk)
* [Boost C++ Libraries](https://www.boost.org)
*Note:* Users reported problems with installing ViennaRNA, so we provide some hints here.
1. Install the [GNU MPFR Library](https://www.mpfr.org) first.
2. Exclude unnecessary components of ViennaRNA:
`./configure --without-swig --without-kinfold --without-forester --without-rnalocmin --without-gsl`
3. If you have linker issues use
`./configure --disable-lto`
4. If your system supports SSE4.1 instructions then we recommend
`./configure --enable-sse`
If you have further suggestions, we are happy to add them here.
## Build instructions
Please create a new directory and build the program for your platform.
1. create a build directory and visit it: `mkdir build && cd build`
2. run cmake: `cmake ../mars`
3. build the application: `make`
4. optional: build and run the tests: `make test`
5. optional: build the api documentation: `make doc`
## Usage
After building the application binary, running Mars is as simple as
```commandline
bin/mars msa.aln -g genome.fasta
```
The resulting genome positions are printed to stdout.
If you want to store the result in a file instead, please use the *-o* option or redirect the output.
```commandline
bin/mars msa.aln -g genome.fasta -o result.txt
bin/mars msa.aln -g genome.fasta > result.txt
```
We recommend you to specify the number of threads with the *-j* option, in order to enable parallel execution.
If you specify *-j 0* the program tries to detect the maximal number of threads available on your machine.
```commandline
bin/mars msa.aln -g genome.fasta -j 0
```
For a list of options, please see the help message:
```commandline
bin/mars --help
```
## Authorship & Copyright
MaRs is being developed by [Jörg Winkler](mailto:[email protected]), but it incorporates a lot of work
from other members of the [SeqAn project](http://www.seqan.de).
You can ask questions and report bugs on the [GitHub tracker](https://github.com/seqan/mars/issues).
Please also [subscribe](https://github.com/seqan/mars/subscription) and/or star us!
You can also follow SeqAn on [Twitter](https://twitter.com/SeqAnLib) to receive updates on MaRs.