RNAlien alternatives and similar packages
Based on the "Bioinformatics" category.
Alternatively, view RNAlien alternatives based on common mentions on social networks and blogs.
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cobot
Computational biology toolkit to collaborate with researchers in constructive protein engineering -
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BlastHTTP
Haskell cabal libary for submission and result retrieval from the NCBI Blast REST webservice -
EntrezHTTP
Haskell cabal libary for submission and result retrieval from the NCBI Entrez REST webservice -
Taxonomy
Haskell cabal Taxonomy libary contains tools, parsers, datastructures and visualisation for the NCBI (National Center for Biotechnology Information) Taxonomy datasources. -
BioHMM
Libary containing parsing and visualisation functions and datastructures for Hidden Markov Models in HMMER3 format. -
StockholmAlignment
Libary containing parsing and visualisation functions and datastructures for Stockholm aligmnent format. -
rank-product
Collects the functions pertaining to finding the rank product of a data set as well as the associated p-value. -
InfluxDB - Power Real-Time Data Analytics at Scale
Do you think we are missing an alternative of RNAlien or a related 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):
Installation via bioconda - recommended
RNAlien can be installed with all tool dependencies via conda. Once you have conda installed simply type:
conda create -n rnalien -c bioconda -c conda-forge rnalienActivate the environment in which RNAlien was installed to use it:
conda activate rnalienTo use the offline-mode of the commandline tool additionally following database downloads are required:
- Download NCBI Taxonomy Dump
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
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:
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 -N4To display the possible commandline options run:
RNAlien --helpFor detailed instruction how to use RNAlien please see the Help page.
- Download NCBI Taxonomy Dump
TaxonomyTools which can be used to visualise the organisms included in a RNAlien result can be found here (License GPL-3):
*Note that all licence references and agreements mentioned in the RNAlien README section above
are relevant to that project's source code only.