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Output format

RNAmmer presents the prediction results in various ways. The main results page (1:see figure below) contains the basic output results in GFF format. In addition the plain-text output data can be obtained as either GFF,XML,HMM report, or FASTA, by following the links on the main result page (2:see figure below).

The GFF file

The GFF file contains the following information
seqname The name of the fasta entry in which the rRNA feature was predicted. The input can contain multiple entries.
source The version of the RNAmmer prediction tool.
feature Always 'rRNA'
start Start position of the rRNA feature
end End position of the rRNA feature
score The HMM alignment score of the calibrated full length model within the window defined by the spotter model
+/- Direction (strand) of the rRNA feature
frame N/A (always '.')
attribute rRNA subunit type (5/8s,16/18s,23/28s rRNA) E-value and score of the HMM alignment of the calibrated full length model within the window defined by the spotter model.

The XML file

Each prediction (corrospond to one line in the GFF) is represented as an entry in the XML file (see figure below)

mol rRNA subunit type (5/8s,16/18s,23/28s rRNA)
feature Always 'rRNA'
start Start position of the rRNA feature
stop End position of the rRNA feature
direction Direction (strand) of the rRNA feature
score The HMM alignment score of the calibrated full length model within the window defined by the spotter model.
evalue The HMM alignment E-value of the calibrated full length model within the window defined by the spotter model.
sequenceEntry The name of the FASTA sequence entry in which the feature has been predicted
sequence The raw DNA sequence of the rRNA gene
model_string The HMM consensus sequence = the highest probability amino acids. Capital letters equal to the highly conserved residues (probability > 0.9)
match_string Letters are exact matches to the consensus sequence. '+' means positive score
query_string The query sequence itself



HMM report file

This is the RAW output of the HMM search program for the window defined by the spotter model. See the HMMer User's Guid

FASTA file

The rRNA gene sequence (DNA) in fasta format.

EXAMPLE OUTPUT

Click here to see an example output of RNAmmer


CORRESPONDENCE

Peter Fischer Hallin:        Karin Lagesen: