e-mail from Kathy 2-5-12

2013-12-01

azim58 - e-mail from Kathy 2-5-12

motif similarity visualization?
2 messages

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Kurt Whittemore <kurtwhittemore@gmail.com>
 Thu, Mar 1, 2012 at 9:28 AM

To: Phillip Stafford <phillip.stafford@asu.edu>
Cc: Kathryn Sykes <Kathryn.Sykes@asu.edu>, Luhui Shen <lshen8@asu.edu>

Hi Phil, Shen and I are planning out how to turn our SMC1fs peptide work
into a paper. We are considering whether or not to make a figure showing
how the different random peptides have different or the same motifs or
whether we should just discuss this information in the text.

* GLAM2 reveals the epitopes in the random peptides that match with the
  original antigen
o TISKY peptide contains two epitopes with HEE and Y. . . PQRE
o AVSHQ peptide contains pqregs
o RVGEM peptide contains empqre
o TAFY peptide contains he

* glam2 score given by comparing original antigen with random peptide
TISKY 7.85694
AVSHQ 7.15938
RVGEM 7.12031
TAFY 5.78213
This shows that TISKY and TAFY both contain the HE motif, whereas TISKY,
AVSHQ, and RVGEM all contain the PQRE motif. The TISKY peptide, which is
the highest binding peptide on the array contains two motifs in common
with the original antigen (HE and PQRE). Do you think we should try to
present this information in some type of a clustered heirarchical tree (a
very small one I guess)? Or is there another way to visualize this
information? Or should we just discuss this information in the text?

Thanks for any help and information you can offer!

-Kurt

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Kathryn Sykes <Kathryn.Sykes@asu.edu>
 Mon, Mar 5, 2012 at 10:26 AM

To: Kurt Whittemore <Kurt.Whittemore@asu.edu>, Phillip Stafford
<Phillip.Stafford@asu.edu>
Cc: Luhui Shen <lshen8@asu.edu>

I think a simple table should do it. For example, the peptide sequences
can be listed with the common motifs in differently colored. I’ll give
you a few comments on your outlined draft later this afternoon.

From: Kurt Whittemore [mailto:Kurt.Whittemore@asu.edu]

Sent: Thursday, March 01, 2012 9:28 AM

To: Phillip Stafford

Cc: Kathryn Sykes; Luhui Shen

Subject: motif similarity visualization?

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