nail-benchmarks

A collection of reproducible benchmarks for nail

Requirements

You'll need the following available on your system path:

• nail
• MMseqs2
• HMMER3
• easel (comes with HMMER3 distributions)
• the create-profmark binary (comes with HMMER3 distributions)

Download sequence data

This benchmark was originally run using Pfam version 36.0 and Swissprot release-2023_05

To download the data, you can run

$ ./scripts/download-data.sh

which will place Pfam seed alignments & Swissprot sequences in the data/ directory:

$ tree data/
data
├── long-seq
│   ├── query
│   │   ├── 1.query.fa
│   │   ├── 2.query.fa
│   │   ├── 3.query.fa
│   │   ├── 4.query.fa
│   │   ├── 5.query.fa
│   │   └── 6.query.fa
│   └── target
│       ├── 1.target.fa
│       ├── 2.target.fa
│       ├── 3.target.fa
│       ├── 4.target.fa
│       ├── 5.target.fa
│       └── 6.target.fa
├── pfam.sto
├── uniprot.tar.gz
├── uniprot_sprot.dat.gz
├── uniprot_sprot.fasta
├── uniprot_sprot.fasta.ssi
├── uniprot_sprot.xml.gz
└── uniprot_sprot_varsplic.fasta.gz

Build the benchmark

To build the benchmark, run

$ ./scripts/build-benchmark.sh

Run the benchmark

To run the benchmark, run

$ ./scripts/run-all.sh

Produce plots

To produce the plots, run

$ python ./scripts/plots.py ./benchmark/