nucleoseeker 0.1.1

Precision filtering of RNA databases to curate high-quality datasets

NucleoSeeker - Precision filtering of RNA databases to curate high-quality datasets

Note: NucleoSeeker currently supports Unix-based systems, including macOS.

Dependencies

NucleoSeeker relies on a few external command-line tools. Before running the software, ensure these tools are properly installed on your system.

Dependency	Minimum Version	Installation Guide
Clustal Omega	1.2.4	Clustal Omega Setup Instructions
Infernal	1.1.5	Infernal Setup Instructions
Emboss	6.6.0	Emboss Setup Instructions (Optional)

Quick Installation Instructions

Install Clustal Omega

• Instructions to setup clustal-omega can be found here.
• Clustal omega version supported 1.2.4

  wget http://www.clustal.org/omega/clustal-omega-1.2.4.tar.gz
  tar zxf clustal-omega-1.2.4.tar.gz
  cd clustal-omega-1.2.4
  ./configure --prefix /your/install/path
  make
  make check                 # optional: run automated tests
  make install               # optional: install Infernal programs, man pages

  # or use this

  sudo apt-get install clustalo

Install Emboss (Optional)

• NOTE - Emboss is very slow, unless you are experimenting we don't recommend using it. Clustal Omega should be sufficient for most use cases.
• For setting up Emboss, please read here.
• Emboss version supported 6.6.0

Install Infernal

• For infernal follow instructions here.
• Infernal version supported 1.1.5

  wget http://eddylab.org/software/infernal/infernal.tar.gz
  tar zxf infernal.tar.gz
  cd infernal-1.1.5
  ./configure --prefix /your/install/path
  make
  make check                 # optional: run automated tests
  make install               # optional: install Infernal programs, man pages

  # or use this

  sudo apt-get install infernal infernal-doc

Get Rfam.cm file ready

• To use this tool, you need to provide the Rfam covariance model which is available for download at https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.cm.gz. It also needs to be modified using cmpress command from Infernal tool (mentioned above). If you don't have it then use the code below -

  cd nucleoseeker
  mkdir -p rfam
  wget https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.cm.gz -O Rfam.cm.gz
  gunzip Rfam.cm.gz
  cmpress Rfam.cm
  

Generating new dataset

After the preliminary steps, a new dataset can be generated by installing NucleoSeeker as follows:

# We recommend setting up a virtual env when using the this tool

python3 -m venv nucleoseeker_env
source nucleoseeker_env/bin/activate
pip install nucleoseeker

After you have prepared the environment you can generate datasets using the following code

export DATA_PATH=/your/desired/path/to/save/the/dataset
nucleoseeker \
        --dataset_name test_dataset \
        --rfam_cm_path your/rfam/path \
        --exptl_method "X-RAY DIFFRACTION" \
        --resolution 3.6 \
        --year_range 2019 \
        --dend 500
        --save 1 \

After using this command, a directory with the name test will be created in the DATA_PATH directory with the following structure:

      ├── DATA_PATH
      ├── pdb_files
      ├── test_dataset
          ├── files
          ├── sequences
          ├──clean_tblout.tblout
          ├──cmscan.out
          ├──combined.fasta
          ├──fam_pdb_chain.csv
          ├──final.fasta
          ├──raw_experimental_RNA_0_500.csv
          ├──sequence_identity_mat_clustal.csv
          ├──tblout.tblout

• raw_experimental_RNA_0_500.csv: Data for first 500 results from the PDB database.

• combined.fasta: Sequences used in sequence identity calculation by Clustal Omega and Emboss, obtained after applying StructureLevelFilter and PDBFilter on the raw data.

• sequence_identity_mat_clustal.csv: Sequence identity matrix obtained from Clustal Omega and Emboss tools.

• final.fasta: Final sequences in fasta format; the output if family analysis is not required.

• cmscan.out, tblout.tblout, clean_tblout.tblout: Output files of the Infernal tool.

• fam_pdb_chain.csv: Mapping of family and PDB chain, obtained after family search by Infernal; the final output for family analysis.

• test_dataset/files: Directory containing dataframes and lists for structures at each filter level.

• test_dataset/sequences: Directory containing sequences for all final structures in individual fasta files.

For some simple examples, please take a look at the this notebook.