Create hmm file - zellerlab/stag GitHub Wiki

You can find hmm files from:

• EggNOG
• PANTHER

If your gene of interest is not there, you can create an hmm file from your reference sequences.

You will need muscle (can be installed through conda with: conda install -c bioconda muscle) and HMMER (can be installed with: conda install -c bioconda hmmer).

Here we use as example test/sequences.fasta.

First, we align the sequences to create a multiple sequence alignment:

muscle -in test/sequences.fasta -out test/sequences.ali

Second, we build a hmm file:

hmmbuild test/gene.hmm test/sequences.ali 

Now test/gene.hmm is ready to be used for the -a input of stag train.