Feature map of a synthetic operonΒΆ

This script shows how to create a picture of an synthetic operon for publication purposes.

../../../_images/sphx_glr_operon_map_001.png
# Code source: Patrick Kunzmann
# License: BSD 3 clause

import matplotlib.pyplot as plt
import biotite
from biotite.sequence import Annotation, Feature, Location
import biotite.sequence.graphics as graphics

strand = Location.Strand.FORWARD
prom  = Feature("regulatory", [Location(10, 50, strand)],
                {"regulatory_class" : "promoter",
                 "note"             : "T7"})
rbs1  = Feature("regulatory", [Location(60, 75, strand)],
                {"regulatory_class" : "ribosome_binding_site",
                 "note"             : "RBS1"})
gene1 = Feature("gene", [Location(81, 380, strand)],
                {"gene" : "gene1"})
rbs2  = Feature("regulatory", [Location(400, 415, strand)],
                {"regulatory_class" : "ribosome_binding_site",
                 "note"             : "RBS2"})
gene2 = Feature("gene", [Location(421, 1020, strand)],
                {"gene" : "gene2"})
term = Feature("regulatory", [Location(1050, 1080, strand)],
                {"regulatory_class" : "terminator"})
annotation = Annotation([prom, rbs1, gene1, rbs2, gene2, term])

fig = plt.figure(figsize=(8.0, 0.8))
ax = fig.add_subplot(111)
graphics.plot_feature_map(
    ax, annotation, multi_line=False, loc_range=(1, 1101),
)
fig.tight_layout()
plt.show()

Gallery generated by Sphinx-Gallery