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Sequence Logos #12
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In GitLab by @szabogtamas on Jan 24, 2020, 20:08 marked the task What sequences to use (TCRA/B primary only?) as completed |
In GitLab by @szabogtamas on Jan 24, 2020, 20:08 marked the task What sequences to use (TCRA/B primary only?) as incomplete |
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. |
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. |
in sc-best-practices, they use the |
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:
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