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.
cinful, a pipeline to identify microcins along with their associated immunity proteins and export machinery, uses PyHMMER to build HMMs from MAFFT-derived alignments, and to run
BUSCOlite, a package for running simplified BUSCO analysis for gene prediction, uses PyHMMER to discover Conserved Orthologous Genes.
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.
GSub, a GUI for submitting viral sequences to GenBank, uses PyHMMER to detect potential polymerase-encoding ORFs.
If you use PyHMMER in a scientific context, feel free to open a pull request to add yourself to the list!
The pytrimal documentation contains an example for building an HMM with PyHMMER from a trimmed alignment, check it here.
For a more detailed explanation of HMMER features, you should also check the HMMER User’s Guide.