Workflows - RNA Prediction
CAMERA workflows can be used to detect both ribosomal RNA (rRNA) and transfer RNA (tRNA) genes. Two different methods are available to predict rRNA genes: context-specific Hidden Markov Model patterns that incorporate RNA-specific structure predictions (RNAmmer), and simple one-dimensional sequence alignment similarity searches performed using the BLAST algorithm. The program tRNAscan-SE can be used to detect tRNA genes.
These workflows accept a FASTA DNA read file as input and produce three output files: the predicted tRNA sequence, the original sequences masked by “N” for RNA sequence, and finally the predicted RNA coordinate table.
rRNA Prediction (HMMR):
Use HMMR 3.0 to predict rRNA sequences from input DNA reads.
rRNA Prediction (Blastn):
Use Blastn to predict rRNA sequences from input DNA reads.
tRNA Prediction:
Use tRNAscan-SE program to predict tRNA sequences from input DNA reads.
Workflow Components:
The RNA Prediction workflows are composed of several components, including:
- HMMR
- Blastn
- tRNAscan-SE
Notes:
- To adjust default parameters, click on the “Advanced Parameters” tab on the workflow submission form.
- Currently the RNA Prediction workflows do not have a graphical output. Please download the results to your local computer for viewing.