Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/eggzilla/rnalien
RNAlien - unsupervised RNA family model construction
https://github.com/eggzilla/rnalien
bioinformatics covariance-model haskell homology-search rna rna-family
Last synced: 2 months ago
JSON representation
RNAlien - unsupervised RNA family model construction
- Host: GitHub
- URL: https://github.com/eggzilla/rnalien
- Owner: eggzilla
- License: gpl-3.0
- Created: 2013-10-07T19:08:45.000Z (about 11 years ago)
- Default Branch: main
- Last Pushed: 2021-06-08T14:12:18.000Z (over 3 years ago)
- Last Synced: 2023-10-20T19:37:56.777Z (about 1 year ago)
- Topics: bioinformatics, covariance-model, haskell, homology-search, rna, rna-family
- Language: Haskell
- Homepage: http://rna.tbi.univie.ac.at/rnalien/
- Size: 2.5 MB
- Stars: 14
- Watchers: 6
- Forks: 2
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- Changelog: ChangeLog.md
- License: LICENSE
Awesome Lists containing this project
README
=========
RNAlien is a tool for automatic construction of RNAfamily models from a single sequence.
It is available as a commandline tool, for testing or construction of few sequences the webservice can be used.
The source code of RNAlien is open source and available via GitHub and Hackage (License GPL-3):
* [](https://github.com/eggzilla/RNAlien) [](https://travis-ci.org/eggzilla/RNAlien) [](https://hackage.haskell.org/package/RNAlien) [](https://anaconda.org/bioconda/rnalien) [](https://hub.docker.com/repository/docker/eggzilla/rnalien) 
### Installation via bioconda - recommended
RNAlien can be installed with all tool dependencies via [conda](https://conda.io/docs/install/quick.html). Once you have conda installed simply type:
conda create -n rnalien185 -c conda-forge -c bioconda rnalien=1.8.5
Activate the environment in which RNAlien was installed to use it:
conda activate rnalien185
To use the offline-mode of the commandline tool additionally following database downloads are required:
* Download [NCBI Taxonomy Dump](ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz)
```bash
wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz
tar -xzf new_taxdump.tar.gz
```
* Download [NCBI Blast version 5 database](https://ftp.ncbi.nlm.nih.gov/blast/db/v5)
```bash
#After installing and activating the RNAlien bioconda environment use update_blastdb.pl
#Show all available databases
update_blastdb.pl --blastdb_version 5 --showall
#Download the nt_v5 database (~about 70 GB in size)
update_blastdb.pl --blastdb_version 5 nt_v5 --decompress
```
### Usage
After installation with bioconda, activating the environment and downloading the files using the offline mode of the command line tool is recommended.
Following are example calls for the files contained in the test directory of the repository.
Using -c 4 and +RTS -N4 provides 4 cpu threads to the used tool dependencies (e.g. blast,..) and to RNAlien.
* Single fasta input:
```bash
RNAlien -i single.fa -c 4 -j -b /pathto/blast5db/nt_v5 -d single -w /pathto/new_taxdump/taxidlineage.dmp +RTS -N4
```
* Multi fasta input:
```bash
RNAlien -i testmulti.fa -c 4 -j -b /pathto/blast5db/nt_v5 -d single -w /pathto/new_taxdump/taxidlineage.dmp +RTS -N4
```
* Stockholm alignment (with consensus structure) input
```bash
RNAlien -p test.stockholm -c 4 -j -b /pathto/blast5db/nt_v5 -d aln -w /pathto/new_taxdump/taxidlineage.dmp +RTS -N4
```
If you just want to try RNAlien out, or to construct a single family the onlinse mode can be used.
It does not require database downloads and queries the required information from ncbi webservices.
A stable, uninterupted internet connection is mandatory.
* Single fasta input (online-mode):
```bash
RNAlien -i single.fa -c 4 -d onsingle +RTS -N4
```
To display the possible commandline options run:
```bash
RNAlien --help
```
For detailed instruction how to use RNAlien please see the [Help page.](http://rna.tbi.univie.ac.at/rnalien/help)
TaxonomyTools which can be used to visualise the organisms included in a RNAlien result can be found here (License GPL-3):
* [](https://github.com/eggzilla/TaxonomyTools) [](https://travis-ci.org/eggzilla/TaxonomyTools) [](https://hackage.haskell.org/package/RNAlien)