Draw 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 TAT box binding protein.
[1]:
from cogent3.parse import jaspar
_, pwm = jaspar.read("../data/tbp.jaspar")
freqarr = pwm.to_freq_array()
freqarr[:5] # illustrating the contents of the MotifFreqsArray
[1]:
| T | C | A | G | |
|---|---|---|---|---|
| 0 | 0.080 | 0.373 | 0.157 | 0.391 |
| 1 | 0.794 | 0.118 | 0.041 | 0.046 |
| 2 | 0.090 | 0.000 | 0.905 | 0.005 |
| 3 | 0.961 | 0.026 | 0.008 | 0.005 |
| 4 | 0.077 | 0.000 | 0.910 | 0.013 |
[2]:
logo = freqarr.logo()
logo.show(height=250, width=500)
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.
[3]:
from cogent3 import load_aligned_seqs
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.
[4]:
aa = aln.get_translation(incomplete_ok=True)[:120]
logo = aa.seqlogo(width=500, height=200, wrap=50, vspace=0.1)
logo.show()