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license: mit
tags:
- dna
- genomics
- tokenization
---
# EvoLen — token analysis input data
Derived interval files needed to reproduce the token analyses in Section 4 of
*EvoLen: Evolution-Guided Tokenization for DNA Language Model*
([arXiv:2604.08698](https://arxiv.org/abs/2604.08698)).
Analysis code lives in the [`evolen` repository](https://github.com/mtapia-pacheco/evolen)
under `analysis/`.
## Contents
```text
region_beds/
source/ INPUT to the P4 enrichment analysis -- the four genomic
regions, merged and cleaned:
promoters_2kb.clean.merged.bed (28,251 intervals)
enhancers_dels.clean.merged.bed (1,464,531)
exon.clean.merged.bed (402,955)
intron.clean.merged.bed (150,128)
conservation_crossed/ OUTPUT of that analysis, provided for checking: the four
regions crossed with conservation category
{promoter,enhancer,exon,intron}_{conserved,neutral,accelerated}.bed
conservation_{conserved,neutral,accelerated}.bed
simple/ the same four regions without the conservation split
ccre_classes/ ENCODE SCREEN cCRE classes as BED, one file per class
CA, CA-CTCF, CA-H3K4me3, CA-TF, PLS, TF, dELS, pELS
*_balanced.bed are downsampled to the smallest class (26,102)
motifs/motifs.txt JASPAR 2024 vertebrate motifs, thresholded to consensus
sequences (PWM positions at 0.5, wildcards trimmed, <= 12 bp)
```
`region_beds/source/` is what `analysis/enrichment/enrichment_heatmap.py` reads; it
generates the conservation split and the crossed BEDs itself, so
`region_beds/conservation_crossed/` is included only so results can be compared without
re-running. `ccre_classes/` backs the Multi-SCREEN task construction; `motifs/` backs the
P1 motif preservation analysis (Figure 2A).
## Not included — fetch these yourself
Two inputs are public reference data and are not mirrored here.
**hg38 reference genome** (~3.3 GB):
```bash
wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
gunzip hg38.fa.gz && samtools faidx hg38.fa
```
**phyloP conservation scores.** The analysis reads per-chromosome bedGraph, which is a
mechanical conversion of the public bigWig (~70 GB expanded, so it is regenerated rather
than distributed):
```bash
wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP100way/hg38.phyloP100way.bw
# convert per chromosome with UCSC bigWigToBedGraph
bigWigToBedGraph -chrom=chr1 hg38.phyloP100way.bw chr1.bedGraph
```
Point `process_bedgraph_all.py --bedgraph_dir` at the directory of resulting
`.bedGraph` files to produce the `{chrom}_phylop_segment.csv` files that drive both
tokenizer construction and the phyloP analyses.
## Usage
```bash
export EVOLEN_ROOT=/path/to/your/data_root # analysis scripts resolve paths from this
```
Related: [token_evaluation](https://huggingface.co/datasets/nancyH/token_evaluation)
hosts the phyloP analysis *outputs* (per-token aggregates used for Figure 2C).
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