RNAmmer¶
Description¶
RNAmmer predicts ribosomal RNA genes in full genome sequences by util- ising two levels of Hidden Markov Models: An initial spotter model searches both strands. The spotter model is constructed from highly conserved loci within a structural alignment of known rRNA sequences. Once the spotter model detects an approximate position of a gene, flanking regions are extracted and parsed to the full model which matches the entire gene. By enabling a two-level approach it is avoided to run a full model through an entire genome sequence allowing faster predictions.
Environment Modules¶
Run module spider rnammer to find out what environment modules are available for this application.
Environment Variables¶
- HPC_RNAMMER_DIR - installation directory
- HPC_RNAMMER_BIN - executable directory
- HPC_RNAMMER_DOC - documentation directory
- HPC_RNAMMER_EXE - examples directory
- HPC_RNAMMER_LIB - library directory
Citation¶
If you publish research that uses rnammer you have to cite it as follows:
Categories¶
biology, rna-seq