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Suggested Format for Documenting Synteny

| posted 12 Jun, 2018 02:28
I had a chance at the annual Faculty Meeting to review a genome Claire Rinehart annotated and found he had a very elegant system for recording synteny arguments. I wanted to share that with the community with the minor modification of also adding three reference phages which demonstrate the synteny in question.

Simpliphy gp 36 - called as Lysin B
Synteny: Lysin A (33) - Holin (34) - Lysin B (36) (MadamMonkfish (E), NoSleep (E), Ukulele (E))

The letters next to the phage names are cluster designations. I find the format elegant and informative. If Welkin and the rest of the community find it useful, we can have it added to the Bioinformatics guide.

Hope this is useful!
| posted 12 Jun, 2018 02:30
I realized I forgot to add one clarification: the numbers next to the gene names in the synteny indicate the phage gp designation. In this example you can surmise that there is a gene between Holin and Lysin B which is not relevant to the three genes in question. I find this more straightforward than simply noting what's directly adjacent to the gene in question.
| posted 17 Jul, 2018 16:22
Thanks for sharing— I agree, that is a nice way of noting things.
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