> For the complete documentation index, see [llms.txt](https://lulab1.gitbook.io/training/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://lulab1.gitbook.io/training/archive/archive-2019/part-iii.-case-studies/case-study-3.deepshape/3.2-resources.md).

# 3.2 Resources

## Databases

* Rfam: (<https://rfam.xfam.org/>)
* Compative RNA Web: (<http://www.rna.icmb.utexas.edu/>)
* RNA STRAND: (<http://www.rnasoft.ca/strand/>)
* bpRNA: (<http://bprna.cgrb.oregonstate.edu/>)
* RNAStralign: (<https://rna.urmc.rochester.edu/pub/RNAStralign.tar.gz>)
* JASPAR (TF motifs): (<http://jaspar.genereg.net/>)

## Data

* **Known structure**: /BioII/lulab\_b/shared/projects/RNA\_known\_structure
* **icSHAPE**: /BioII/lulab\_b/shared/projects/icSHAPE
* **RNAex (DMS-seq, PARS, icSHAPE)**: /BioII/lulab\_b/shared/projects/RNAex
* **SHAPE-MaP**: /BioII/lulab\_b/shared/projects/shape-map
* **RNAStralign**: /BioII/lulab\_b/shared/projects/RNA\_stralign

## Software

* **icSHAPE pipeline**: (<https://github.com/qczhang/icSHAPE>)
* **ShapeMapper 2**: (<https://github.com/Weeks-UNC/shapemapper2>)
* **ShaperMapper**: (<https://weeks.chem.unc.edu/software-files/ShapeMapper_v1.2.tar.gz>)
* **Superfold (SHAPE-MaP)**: (<https://weeks.chem.unc.edu/software-files/Superfold_v1.0.tar.gz>)

## Scripts

### Predict SHAPE data

Project directory: `/Share2/home/lulab/shibinbin/projects/Deepfold2`

Files:

* **Scripts**: `bin/`
* **icSHAPE data preprocessing**: `Jobs/icSHAPE_*.sh`
* **Notes**: `notes/*.md`
* **Processed icSHAPE data**: `output/icSHAPE_preprocess/`
* **icSHAPE reactivities in HDF5 format**: `data/icSHAPE/`
* **Prediction using neural network**: `bin/predict_reactivity.py`
* **Neural network models (keras)**: `models/`
* **Workflows using snakemake**: `workflows/`
* **Predict RNA-protein binding**: `output/motif_ionmf`
* **Jupyter notebooks**: `jupyter/`

### Motif discovery

Project directory: `/Share2/home/lulab/shibinbin/projects/DeepShape`

* **Scripts**: `bin/`
* **Notes**: `notes/`
* **Training and test data**: `output/rfam/`, `output/jaspar/`

## Work reports

Tsinghua Cloud (<https://cloud.tsinghua.edu.cn>):

Summary slide: DeepShape summary 20190622.pptx

```
Lu Lab / Lu Lab Shared / 1.Project Progress / 14' Shi Binbin / DeepShape
```