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.. jupyter-execute::
:hide-code:
import set_working_directory
Sequence logos
==============
Sequence logo's display sequence information. They're extensively applied to transcription factor binding site (TFBS) display. They can also be applied to sequence alignments more generally.
Drawing logo for a TFBS
-----------------------
We use the TFBS for the TATA box binding protein.
.. jupyter-execute::
from cogent3 import load_aligned_seqs
from cogent3.parse import jaspar
_, pwm = jaspar.read("data/tbp.jaspar")
freqarr = pwm.to_freq_array()
freqarr[:5] # illustrating the contents of the MotifFreqsArray
.. jupyter-execute::
logo = freqarr.logo()
logo.show(height=250, width=500)
.. jupyter-execute::
:hide-code:
outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-seqlogo.png"
logo.write(outpath)
Drawing a sequence logo from a multiple sequence alignment
----------------------------------------------------------
This can be done for an entire alignment, but bear in mind it can take some time to render. Note that we include gap characters in the display.
.. jupyter-execute::
aln = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna")
l = aln[:311].seqlogo(height=300, width=500, wrap=60, vspace=0.05)
l.show()
Sequence logo of protein alignment
----------------------------------
No difference here except it uses the built-in colour scheme from the protein ``MolType``.
.. jupyter-execute::
aa = aln.get_translation(incomplete_ok=True)[:120]
logo = aa.seqlogo(width=500, height=300, wrap=50, vspace=0.1)
logo.show()
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