Home

prot2exon

Map protein-domain amino-acid coordinates to their underlying genomic CDS/UTR/intron structure, using any Ensembl, GENCODE, or NCBI RefSeq GTF.

For each input query (a protein_id or a transcript_id, optionally with an aa range), prot2exon answers two related but distinct questions:

1. Mapping — which exact genomic bases code this domain?
2. Structure / visualization — how is the whole transcript organised in 5′UTR / CDS / 3′UTR / intron, and where does the domain fall on it?

A C++17 binary does the heavy lifting (≤ 1 µs per query on a warm index), a Python wrapper gives you DataFrames, and a plot subcommand renders matplotlib / plotly / a vanilla-JS standalone HTML viewer.

Wiki navigation

Page	What's on it
Installation	Build the C++ binary, install the Python wrapper, Docker.
Quickstart	End-to-end in five commands.
Input format	BED-like input, ENSP vs ENST, no-domain mode, prep scripts.
Output modes	coding / introns / span / isoform / bed12 / all.
Plotting and viewers	matplotlib, plotly, the interactive HTML viewer, Jupyter embed.
Genome onboarding	prot2exon fetch, manual recipes, GTF compatibility.
Custom proteins	Append unannotated proteins (transgenes, non-reference ORFs, …) to an existing GTF.
Python API	Mapper, MappingResult, plot, render_interactive_jupyter.
CLI reference	Every CLI flag at a glance: map, plot, fetch.
Notebooks	The three worked-example notebooks shipped under notebooks/ — walkthrough, Pfam atlas, ClinVar enrichment.
Validation	100 % exact match vs ensembldb on 5,000 stratified queries — design, results, gotchas.
Benchmarks	4-tool head-to-head (prot2exon, ensembldb, TransVar, Ensembl REST), scaling, parallel scaling.
Performance and RAM	--threads, --batch-size, 1 M-query benchmark.
Architecture	What lives where: parser, mapper, writer, index format.
FAQ	Common gotchas: CDS-length mismatch, MANE Select, "index already exists", ...

Project links

• Repository: https://github.com/SotoLF/Prot2Exon
• Owner: Luis F. Soto Ugaldi (@SotoLF)
• Collaborator: George D. Muñoz Esquivel (@george123ya)
• Issue tracker: open a ticket on the same repo.
• Citation: see the bottom of FAQ.