Method | Sequence motif | Structure motif | Model | Code | Reference |
---|---|---|---|---|---|
MEMERIS | Yes | No | Maximum likelihood estimation | [2] | |
BEAM | No | Yes | Simulated annealing | [10] | |
CapR | No | Yes | Turner energy model | [11] | |
Li et al. | Yes | Yes | Iterative refinement | - | [3] |
GraphProt | Yes | Yes | Graph encoding | [13] | |
DeepBind | Yes | No | CNNs | [19] | |
DeeperBind | Yes | No | CNNs and LSTMs | [23] | |
RNAcontext | Yes | Yes | probabilistic models | [12] | |
Zeng et al. | Yes | No | CNNs | [24] | |
iDeep | Yes | No | DBNs and CNNs | [28] | |
iDeepV | No | No | CNNs | [22] | |
iDeepE | Yes | No | CNNs | [29] | |
iONMF | Yes | No | matrix factorization | [14] | |
Deepnet-rbp | Yes | Yes | DBNs | [21] | |
DanQ | Yes | No | CNNs and LSTMs | [27] |