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Tools for RNA classification
By Abhinav 536 days ago Comments (1)
barrnap - https://github.com/tseemann/barrnap
CPAT - https://github.com/liguowang/cpat, http://lilab.research.bcm.edu/ (web server)
CPC2 - https://github.com/gao-lab/CPC2_standalone, http://cpc2.gao-lab.org/ (web server)
Infernal - http://eddylab.org/infernal/, https://github.com/EddyRivasLab/infernal
NCBI RefSeq - https://www.ncbi.nlm.nih.gov/refseq/
Rfam - http://rfam.xfam.org/, https://docs.rfam.org/en/latest/index.html
SILVA - https://www.arb-silva.de/
RNAmmer - http://www.cbs.dtu.dk/services/RNAmmer/ (web server, standalone download link)
Comments
There are several tools available for RNA classification, each with its own strengths and limitations. Here are some commonly used tools:
Infernal: Infernal is a popular tool for RNA classification that uses a covariance model approach to identify RNA homologs. It is particularly useful for identifying non-coding RNA (ncRNA) sequences.
Rfam: Rfam is a database of RNA families and their corresponding covariance models. It is based on Infernal and provides a comprehensive resource for RNA classification.
RNAcode: RNAcode is a machine learning-based tool that uses a support vector machine (SVM) algorithm to classify RNA sequences. It is particularly useful for identifying small functional RNA molecules.
RNAmmer: RNAmmer is a tool for predicting rRNA genes in genomic sequences. It uses a combination of HMM-based and BLAST-based approaches to identify rRNA sequences.
tRNAscan-SE: tRNAscan-SE is a tool for identifying tRNA genes in genomic sequences. It uses a combination of HMM-based and comparative sequence analysis approaches to predict tRNA genes.
These tools can be used individually or in combination to achieve the best possible classification of RNA sequences.