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JianiC / RSV_Epitope

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Study the Epitope profile with Phylogenetic methods #2

Open JianiC opened 3 years ago

JianiC commented 3 years ago

why BaTs can be used

study the association between trait state and tree topology with credible intevel. But for sure it si related to tree topology as the epitope perdiction based on the sequence. That's why desease severity or geographic distribution can be studied using BaTs.

epitope phylogeny

Need to clarify the question we want to answer? which method should be used?

available in Beast2 with Bable package but this is designed for linguistic study

Binary CTMC: gamma rates heterogeneity Binary covarion: two state : fast and slow Stochastic Dollo: have difficulty fitting data Psedo Dollo: birth rate and death rate; allow multiple birth compared with SD , allow multistate? Dollo covarion

A test for a small RSV_F dataset (n=137)

BCTMC test tree

RSVB_F_test_anot tree

PD model : hard to converge

JianiC commented 3 years ago

Construct the antigentic cartagraphy with epitope distance?

Screen Shot 2020-09-21 at 5 01 26 PM Screen Shot 2020-09-21 at 5 01 42 PM
JBahl commented 3 years ago

Oh - this is exciting! Are the squares the vaccine candidates? How do you calculate the epitope distances?

J

On Sep 21, 2020, at 5:02 PM, JianiC notifications@github.com<mailto:notifications@github.com> wrote:

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Construct the antigentic cartagraphy with epitope distance? [Screen Shot 2020-09-21 at 5 01 26 PM]https://user-images.githubusercontent.com/47227610/93821151-2eabe800-fc2c-11ea-80ca-7d5a36c73d89.png

[Screen Shot 2020-09-21 at 5 01 42 PM]https://user-images.githubusercontent.com/47227610/93821126-2489e980-fc2c-11ea-9bb6-5fee30243900.png

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/JianiC/RSV_Epitope/issues/2#issuecomment-696374447, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADSPRN53NJBF3WF7SNOIRBTSG65OHANCNFSM4P5AWLAA.

JianiC commented 3 years ago

Oh - this is exciting! Are the squares the vaccine candidates? How do you calculate the epitope distances? J On Sep 21, 2020, at 5:02 PM, JianiC notifications@github.com<mailto:notifications@github.com> wrote: [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Construct the antigentic cartagraphy with epitope distance? [Screen Shot 2020-09-21 at 5 01 26 PM]https://user-images.githubusercontent.com/47227610/93821151-2eabe800-fc2c-11ea-80ca-7d5a36c73d89.png [Screen Shot 2020-09-21 at 5 01 42 PM]https://user-images.githubusercontent.com/47227610/93821126-2489e980-fc2c-11ea-9bb6-5fee30243900.png — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#2 (comment)>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADSPRN53NJBF3WF7SNOIRBTSG65OHANCNFSM4P5AWLAA.

Yes, I am testing a small dataset from Swan, which is a 2019 influenza dataset. I have not try with RSV yer due to an error from the iVAX set, The square are the vaccine strains, and epitope distance is actually an adjusted shared epitope count, and I do think there are other more accurate parameter I need to try.