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:

Lagesen, K., Hallin, P., Rødland, E. A., Stærfeldt, H. H., Rognes, T., & Ussery, D. W. (2007). RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Research, 35(9), 3100-3108. https://doi.org/10.1093/nar/gkm160

Categories¶

biology, rna-seq