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UoB-DSMP-2023-24 / dsmp-2024-g8

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Organize thoughts and outlines with Lesli about data is needed for clustering algorithm. #2

Open Bayan-Alsaghier opened 4 months ago

Bayan-Alsaghier commented 4 months ago

Organize thoughts and outlines with Lesli about data needed for the clustering algorithm. Make sure that the outlines are clear so that we can move forward to Q5 seamlessly. Provide an outline of the required columns and why we need this data, not other data.

williamwenlma commented 4 months ago

The GLIPH algorithm requires sequence data of T-cell receptors (TCRs), as well as related HLA data. Specifically, GLIPH uses global and local TCR sequence similarity, structural tendencies of antigenic peptide contact, V segment preferences, CDR3 length preferences, and shared HLA among TCR contributors to identify and cluster TCR sequences with similar specificity.

Below are several key steps in the implementation of GLIPH clustering: 1、Sequence Similarity Analysis 2、Shared Motif Identification 3、Local and Global Clustering 4、Statistical Significance Assessment

ref: https://www.nature.com/articles/nature22976