SEA-PHAGES | Suggested Format for Documenting Synteny

Suggested Format for Documenting Synteny

Link to this post \| posted 12 Jun, 2018 02:28
jdiaz	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!

Link to this post | 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!

Link to this post \| posted 12 Jun, 2018 02:30
jdiaz	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.

Link to this post \| posted 17 Jul, 2018 16:22
welkin	Thanks for sharing— I agree, that is a nice way of noting things.

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Suggested Format for Documenting Synteny