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)
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
Last updated