Examples

Analyses

This section of the documentation shows several examples adapted from real examples, and running with the latest version of the PyHMMER interface.

Analyses

• Build an HMM from an multiple sequence alignment
  • Loading the alignment
  • Building an HMM
  • Saving the resulting HMM
  • Applying the HMM to a sequence database
• Analyse the active site of an enzymatic domain
  • Loading the HMM
  • Loading digitized sequences
  • Running a search pipeline
  • Rendering the alignments
  • Checking individual positions for catalytic activity
• Fetch marker genes from a genome
  • Getting the cutoffs
  • Downloading the HMMs
  • Loading the sequences
  • Running the search pipeline
  • Filtering results
• Run an iterative search to build a HMM for rhodopsins
  • Downloading sequence data
  • Running a simple search
  • Running a conservative iterative search
  • Running an iterative search with custom selection
  • Recording bitscore cutoffs
  • Saving the HMM

Code & Data

This section shows more practical tutorials about how you can use the PyHMMER API in combination with Python and other Python libraries:

Code & Data

• Recipes for extending PyHMMER
  • Loading multiple HMMs
• Create a Python package with embedded HMMs
  • Overview
  • Folder structure
  • Loading data from Python
  • Distributing data
• Improve performance with some tips
  • Storing HMMs
  • Search and scan
  • Pre-fetching the target database

Dependent projects

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 hmmsearch.

• 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.

• Bakta, a standardised annotation tool for bacterial genomes and plasmids, uses PyHMMER to annotate genes with different HMM libraries such as AntiFam or Pfam.

• Pharokka, a rapid standardised annotation tool for bacteriophage genomes and metagenomes, uses PyHMMER to annotate genes with the PHROGS HMMs.

Hint

If you use PyHMMER in a scientific context, feel free to open a pull request to add yourself to the list!

External resources

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.