Rna Structure Python Packages

rna-tools

🔧rna-tools: a toolbox to analyze sequences, structures and simulations of RNA (and more) used by RNA CASP, RNA PUZZLES, and me ;-) docs @ http://rna-tools.rtfd.io web @ http://rna-tools.online

diffbio

End-to-end differentiable bioinformatics for JAX/Flax NNX: soft Smith-Waterman alignment, read mapping and assembly, variant calling, RNA-seq, single-cell, epigenomics, CRISPR, metabolomics, multi-omics, protein and RNA structure, molecular dynamics and drug-discovery operators composed into trainable pipelines on the Avitai stack.

ostir

Software for predicting translation initiation rates in bacteria

squarna

RNA secondary structure prediction tool

barnaba

Analyse Nucleic Acids Structure and Simulations with baRNAba

rna-structure-audit

Three-rung benchmark for whether RNA/DNA foundation models encode secondary structure or composition shortcuts. Preregistered; every figure in the paper is re-derived from the deposited results by a script here.

segshape

RNA secondary structure prediction from Nanopore direct RNA sequencing.

bialign

Bialignment of RNAs and proteins

artem-rna

RNA/DNA 3D structure alignment tool

molprisma

Tool for fast inspection of PDB molecular files inside the terminal.

predted

predTED — Fast approximate Tree Edit Distance (TED) prediction for RNA secondary structures using LightGBM. Up to 100x faster than exact TED computation.

seismic-graph

Plotting engine for SEISMIC-RNA