{ "cells": [ { "cell_type": "markdown", "id": "c9467c38", "metadata": {}, "source": [ "# Fetch marker genes from a genome" ] }, { "cell_type": "markdown", "id": "094d9734", "metadata": {}, "source": [ "This example is adapted from the [fetchMGs](https://github.com/motu-tool/fetchMGs/blob/master/fetchMGs.pl) Perl script used in [mOTU](https://motu-tool.org/) to extract the 40 single-copy universal marker genes from a genome, annotating proteins to find the highest scoring proteins mapping to each of these marker genes.\n", "\n", "In this notebook, we show how to reproduce this kind of analysis, using `pyhmmer` instead of HMMER3 to perform the alignments and extract the bit scores.\n", "\n", "