Author: Marcin Gradowski, Marianna Krysińska

The script auto_HMM_beta.py automates the processing of protein sequences in FASTA format. It splits sequences into shorter and longer ones based on a specified length threshold, clusters similar sequences using CD-HIT, aligns them with Clustal Omega, and builds Hidden Markov Model (HMM) profiles using HMMER.

• Python 3.6+
• Biopython
• CD-HIT
• Clustal Omega (clustalo)
• HMMER (hmmbuild)

1. Clone the repository:

   git clone https://github.com/username/auto_HMM_beta.git
   cd auto_HMM_beta

2. Install Python dependencies:

   pip install biopython

3. Ensure the following tools are installed and accessible in your PATH:

   cd-hit clustalo hmmbuild

python auto_HMM_beta.py

Default parameters:

• cutoff (sequence length): 50
• cd_hit_threshold (CD-HIT similarity threshold): 0.80
• cd_hit_word_length (CD-HIT word length): 5

You can modify these parameters directly in the script or by specifying command-line arguments if implemented.

/ShortsAndLong/      # Results of sequence splitting
/Clustered/          # CD-HIT clustering outputs
/ClustalO/           # Aligned FASTA files
/HMM/                # Generated HMM profiles
HMM_names.txt        # List of HMM profile names and metadata

BSD 2-Clause "Simplified" License