NoMoCLIP

Interpretable Modeling of RNA–Protein Interactions from eCLIP‑Seq Profiles for Motif‑Free RBPs

1. Data availability

NoMoCLIP_dataset

2. Environment Setup

2.1 Create and activate a new virtual environment

conda create -n NoMoCLIP python=3.7.16 
conda activate NoMoCLIP

2.2 Install the package and other requirements

pip install NoMoCLIP
nomoclip install

3. Process data

3.1 Sequential encoding

nomoclip run position_inf  --set_path <PATH_TO_YOUR_DATA>  --out_path <PATH_TO_YOUR_OUTPUT_DIRECTORY>

3.2 Structural encoding

This feature requires the RNAplfold tool, which is executed in a Python 2.7 environment. Please set the --env parameter to the local RNAplfold environment.

nomoclip run structure_inf  --env <NAME_OF_YOUR_ENV>  --set_path <PATH_TO_YOUR_DATA>  --out_path <PATH_TO_YOUR_OUTPUT_DIRECTORY>

3.3 Semantic encoding

nomoclip run attention_graph \
  --kmer 1 \
  --set_path <PATH_TO_YOUR_DATA> \
  --out_path <PATH_TO_YOUR_OUTPUT_DIRECTORY> \
  --model_type <PATH_TO_YOUR_NLP_MODEL> \ 
  --maxlen 101 \
  --device cuda:1 \
  --device1 cuda:1 \
  --device2 cuda:1 

3.4 Functional properties

For this feature, you need to use the corain. Please set the --env parameter to the local corain environment.

nomoclip run instinct_inf \
  --env <NAME_OF_YOUR_ENV> \
  --base_path <PATH_TO_YOUR_DATA> \
  --set_path <PATH_TO_YOUR_INTERMEDIATE_OUTPUT_DIRECTORY> \
  --out_path <PATH_TO_YOUR_OUTPUT_DIRECTORY> \
  --method_path <PATH_TO_YOUR_CORAIN_DIRECTORY> \ 
  --num 2

Note: The argument --num should be tested with all values in [2, 3, 5, 7, 10].

4. Training Process

nomoclip run model_train \
  --base_path <PATH_TO_YOUR_DATA_DIRECTORY> \
  --set_path <PATH_TO_YOUR_FEATURE_DIRECTORY> \
  --out_path <PATH_TO_YOUR_OUTPUT_DIRECTORY> \
  --fold 5  \
  --gpu_id 1

5. Prediction

nomoclip run model_predict \
  --set_path <PATH_TO_YOUR_FEATURE_DIRECTORY> \
  --out_path <PATH_TO_YOUR_OUTPUT_DIRECTORY> \
  --model_path <PATH_TO_YOUR_MODEL> \
  --gpu_id 1

🧬 Motif analysis

Motif extraction requires the installation of the MEME Suite package.

6.1 Sequential motifs

nomoclip run seq_motifs \
  --layer <THE_LAYER_OF_MODEL_YOU_SELECTED> \
  --set_path <PATH_TO_YOUR_FEATURE_DIRECTORY> \
  --out_path <PATH_TO_YOUR_OUTPUT_DIRECTORY> \
  --model_path <PATH_TO_YOUR_MODEL> \
  --pwm_path <PATH_TO_YOUR_PWM_FILE> \
  --motif_size 7 \
  --gpu_id 1

6.2 Structural motifs

nomoclip run structure_motifs \
  --layer <THE_LAYER_OF_MODEL_YOU_SELECTED> \
  --set_path <PATH_TO_YOUR_FEATURE_DIRECTORY> \
  --out_path <PATH_TO_YOUR_OUTPUT_DIRECTORY> \
  --model_path <PATH_TO_YOUR_MODEL> \
  --motif_size 7 \
  --gpu_id 1

📊 High attention regions

nomoclip run high_attention_region \
  --set_path <PATH_TO_YOUR_FEATURE_DIRECTORY> \
  --out_path <PATH_TO_YOUR_OUTPUT_DIRECTORY> \
  --model_path <PATH_TO_YOUR_MODEL> \
  --gpu_id 1