Examples ======== Analyses -------- This section of the documentation shows several examples adapted from real examples, and running with the latest version of the PyHMMER interface. .. toctree:: :maxdepth: 2 :caption: Analyses 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: .. toctree:: :maxdepth: 2 :caption: Code & Data Recipes for extending PyHMMER Create a Python package with embedded HMMs Improve performance with some tips 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 `~pyhmmer.hmmer.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 `_.