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.
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
| T | C | A | G | |
|---|---|---|---|---|
| 0 | 0.0797 | 0.3728 | 0.1568 | 0.3907 |
| 1 | 0.7943 | 0.1183 | 0.0411 | 0.0463 |
| 2 | 0.0900 | 0.0000 | 0.9049 | 0.0051 |
| 3 | 0.9614 | 0.0257 | 0.0077 | 0.0051 |
| 4 | 0.0771 | 0.0000 | 0.9100 | 0.0129 |
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.
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.
aa = aln.get_translation(incomplete_ok=True)[:120]
logo = aa.seqlogo(width=500, height=300, wrap=50, vspace=0.1)
logo.show()