---
title: "25-hmmer"
output: html_document
date: "2025-11-01"
---

```{bash}
# Download the latest Pfam-A database (uncompressed ~2 GB)
cd ../data
wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz
gunzip Pfam-A.hmm.gz
```

```{bash}
hmmpress ../data/Pfam-A.hmm
```


```{bash}
hmmscan \
  --cpu 42 \
  --domtblout ../output/25-hmmer/Apul_hmmscan_results.domtblout \
  ../data/Pfam-A.hmm \
  ../data/protein/Apulchra-genome.pep.faa > ../output/25-hmmer/Apul_hmmscan_results.txt
```

```{bash}
hmmscan \
  --cpu 46 \
  --domtblout ../output/25-hmmer/Peve_hmmscan_results.domtblout \
  ../data/Pfam-A.hmm \
  ../data/protein/Porites_evermanni_v1.annot.pep.fa > ../output/25-hmmer/Peve_hmmscan_results.txt
```


```{bash}
hmmscan \
  --cpu 46 \
  --domtblout ../output/25-hmmer/Ptuh_hmmscan_results.domtblout \
  ../data/Pfam-A.hmm \
  ../data/protein/Pocillopora_meandrina_HIv1.genes.pep.faa > ../output/25-hmmer/Ptuh_hmmscan_results.txt
```