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.
The required software must be added to the system path.
- BLAST+ executables: The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.
- Hmmer: HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments.
The downloaded and reformatted newest version of the SILVA SSU and LSU databases are required by "rna2taxon.pl" program to do the taxonomic assignments for the input rRNA gene sequences. The following command can be used to download and generate the databases.
perl make_taxonclassify_db.pl 132
The functionality provided by rRNAFinder.pl can be accessed through the help menu:
>perl rRNAFinder --help
Running rRNAFinder.pl with the default parameters
perl bin/rRNAFinder.pl examples/test.fasta
The functionality provided by rna2taxon.pl can be accessed through the help menu:
>perl rna2taxon.pl --help
Classify the predicated rRNA genes (16S, 18S, 23S, 28S rRNA genes) with default parameters
perl rna2taxon.pl --dbtype ssu 16SrRNA.ffn
perl rna2taxon.pl --dbtype lsu 23SrRNA.ffn