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

2 messages
 * motif similarity visualization?**

Cc: Kathryn Sykes , Luhui Shen  ||
 * **Kurt Whittemore ** || **Thu, Mar 1, 2012 at 9:28 AM** ||
 * To: Phillip Stafford 
 * || 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.

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 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?
 * GLAM2 reveals the epitopes in the random peptides that match with the original antigen
 * glam2 score given by comparing original antigen with random peptide

Thanks for any help and information you can offer!

-Kurt ||  ||

Cc: Luhui Shen  ||
 * **Kathryn Sykes ** || **Mon, Mar 5, 2012 at 10:26 AM** ||
 * To: Kurt Whittemore , Phillip Stafford 
 * || 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? ||  ||