RMDetect fails to recognize any motif in the example lysine riboswitch sequence:
$ python2 rmdetect.py --data-path models --out lys_result.txt examples/lysine/lys.seq
Searching for models in:
1. '--data-path' option: OK! -> 'models'
Loading models from: 'models' ....
Included models: TGA_1.0, KT_1.0, GB_1.0, CL_1.0
Excluded models: none
Scanning 1 sequences...
Sequence 1 of 1 'unique'slide pos 76 of 194
DONE
$ python2 rmout.py --data-path models < lys_result.txt
Searching for models in:
1. '--data-path' option: OK! -> 'models'
Loading models from: 'models' ....
Included models: TGA_1.0, KT_1.0, GB_1.0, CL_1.0
Excluded models: none
Reading data from results file: None
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Found 0 candidates:
# sequence model ver. score bpp pos cols motif
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It seems that RMDetect correctly loads models for kink-turn and G-bulged modules, but is unable to find them in the given sequence. This is incorrect according to supplementary materials of the main RMDetect paper: https://static-content.springer.com/esm/art%3A10.1038%2Fnmeth.1603/MediaObjects/41592_2011_BFnmeth1603_MOESM173_ESM.pdf
According to it, the output should be:
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Found 2 candidates:
# sequence model ver. score bpp pos cols motif
1 unique KT 1.0 14.27 0.45 35-51 35-51 GUGAGG-CCAGAGA.CC
2 unique GB 1.0 6.88 0.09 23-65 23-65 CAGGUA.G-UGAGGG
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What is the reason? Why cannot RMDetect find the modules?
RMDetect fails to recognize any motif in the example lysine riboswitch sequence:
It seems that RMDetect correctly loads models for kink-turn and G-bulged modules, but is unable to find them in the given sequence. This is incorrect according to supplementary materials of the main RMDetect paper: https://static-content.springer.com/esm/art%3A10.1038%2Fnmeth.1603/MediaObjects/41592_2011_BFnmeth1603_MOESM173_ESM.pdf
According to it, the output should be:
What is the reason? Why cannot RMDetect find the modules?