rRNAFinder

rRNAFinder is a small perl software package, which can be used to automatically predict and classify the ribosome RNA genes using the assembled genome/metagenome contigs as input. The software were only tested on the Linux operating system.

"rRNAFinder.pl" program included in the package uses nhmmer program searching against the arc.hmm, bac.hmm, and euk.hmm databases to identify rRNA genes from the input contigs. The predicated rRNA genes include 16S, 18S, 23S, 28S, 5S, and 5.8S rRNA genes.

The "rna2taxon.pl" program accepts the above generated fasta format rRNA gene sequences as an input to produce the taxonomic assignments for the input genes. The input rRNA gene sequences are searched against the downloaded and reformatted SILVA SSU and LSU databases using blastn.

Please refer to the README.md file from rRNAFinder GitHub repository located at https://github.com/xiaoli-dong/rRNAFinder for instructions on configuring and running rRNAFinder

Features

Predict rRNA genes (5s, 5.8s, 16s, 18s, 23s, 28s rRNA genes)
Taxonomic assignment of the predicted rRNA genes using blastn search against SILVA SSU and LSU databases
Fast and can use multiple CPU threads

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Additional Project Details

Operating Systems

Linux

Intended Audience

Science/Research

User Interface

Command-line

Registered

2018-05-30

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