This section of the documentation shows several examples adapted from real examples, and running with the latest version of the PyHMMER interface.
- Build an HMM from an multiple sequence alignment
- Analyse the active site of an enzymatic domain
- Fetch Marker Genes from a genome
- Run an iterative search to build a HMM for rhodopsins
Code & Data¶
This section shows more practical tutorials about how you can use the PyHMMER API in combination with Python and other Python libraries:
PyHMMER is being used in several projects, including:
GECCO, a tool for detecting Biosynthetic Gene Clusters in genomic data, uses PyHMMER to annotate proteins with Pfam domains to use as sequence features for a machine learning model.
BiG-SLICE, an interactive tool for the large scale analysis of Biosynthetic Gene Clusters data, uses PyHMMER for the Pfam domain annotation step.
duomolog, a method to identify the best set of homologous sequences from two homology searching approaches, uses PyHMMER to search for homologous sequences before comparing the results to BLAST hits.
FastAAI, a package providing fast estimation of Average Amino Acid Identities (AAI) for bacterial and viral genomes, uses PyHMMER to detect bacterial and archaeal domains.
SADIE, the Sequencing Analysis and Data library for Immunoinformatics Exploration, uses PyHMMER as an aligner backend to re-number sequence alignment columns.
If you use PyHMMER in a scientific context, feel free to open a pull request to add yourself to the list!
For a more detailed explanation of HMMER features, you should also check the HMMER User’s Guide.