Sequence Logos

[grst]

In GitLab by @grst on Jan 24, 2020, 14:06

Here's a quite recent re-implementation of sequence logos in Python that looks promising:
https://github.com/jbkinney/logomaker

We will also require an algorithm for multiple sequence alignment in addition to the pairwise one that we have already.

Things to discuss:

• What sequences to use (TCRA/B primary only?)
• What happens if a cell lacks the alpha/beta chain?

[grst]

In GitLab by @szabogtamas on Jan 24, 2020, 20:08

marked the task What sequences to use (TCRA/B primary only?) as completed

[grst]

In GitLab by @szabogtamas on Jan 24, 2020, 20:08

marked the task What sequences to use (TCRA/B primary only?) as incomplete

[grst]

In GitLab by @szabogtamas on Jan 24, 2020, 20:13

For sequence logos I would consider the primary alpha+beta only. The only exception is groups made with tcrdist maybe. Here, I would want to show a sequence logo of the closest chains that are not necessarily the primary alpha and beta.

[grst]

In GitLab by @szabogtamas on Jan 24, 2020, 20:14

As to the lacking chains: I would just mark them with 'XXXXXXXXXXXXXXXX' just like for sequence alignment. But this is only an initial idea, maybe we can come up with something better later on.

[grst]

Possibly also include V & D genes into sequence logo.

Example from Dash et al. (2017):

[grst]

in sc-best-practices, they use the palmotif library. It looks pretty straightforward
https://www.sc-best-practices.org/air_repertoire/clonotype.html#motif-sequence-analysis