eggzilla/RNAlien

rna rna-family covariance-model homology-search haskell bioinformatics

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):

Installation via bioconda - recommended

RNAlien can be installed with all tool dependencies via conda. 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
```
   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
```
   #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:
```
   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:
```
   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
```
   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):
```
   RNAlien -i single.fa -c 4 -d onsingle +RTS -N4
```
To display the possible commandline options run:
```
   RNAlien --help
```
For detailed instruction how to use RNAlien please see the Help page.