pre-mRNA_SecStruct

Computational modeling for sequence and structural features of yeast pre-mRNA

Overview

This repository contains:

• Database with gene annotations, RNA-seq RPKMs, intron sets in S. cerevisiae, alignments across Saccharomyces genus
  • Each intron set (e.g. standard introns, controls, decoys, proto introns) includes:
    • sequences
    • splice site positions
    • cached secondary strucure features
    • minimum free energy secondary structures
    • stochastically sampled secondary structure ensembles (will be stored here but not uploaded to repo)
• Feature calculation:
  • transcription levels
  • stop-codon features
  • sequence-based features: splicing motifs PWMs, length distributions
  • secondary structure features: stem dGs, longest stem, maximum path length, sequence protection
• Basic utilities:
  • Conversions between Refseq / Ensembl / symbolic gene names
  • Secondary structure and ensemble generation
  • Processing sequence alignments
• Cache expensive-to-compute secondary structure ensembles and features
• Analyses:
  • Statistical comparisons between intron and control / decoy sets
  • Analyzing sequence and secondary structure properties across yeast species
  • Identifying decoy introns from whole transcriptome
  • Classification of introns vs decoys

Generating figures

A description for how to generate figures is included in src/README.md.

Requirements

• scipy v1.10.1
• numpy v1.24.3
• matplotlib v3.7.1
• seaborn v0.12.2
• pandas v2.0.2
• sklearn v1.3.0
• argparse v1.1
• mygene v3.2.2
• arnie: https://github.com/DasLab/arnie
• RNAstructure v6.2: https://rna.urmc.rochester.edu/RNAstructureDownload.html
• Vienna 2.0: https://www.tbi.univie.ac.at/RNA
• Contrafold 2.00: http://contra.stanford.edu/contrafold/download.html

Installation

• Install all requirements (expected time: 1-2 hours)
• Clone repository
• Copy src/sample_config.py to src/config.py and update paths.