how to identify cores, accesory and unique sequences from proteomes

Question

[kamel]

Hi, I have 8 proteomes in multifasta format, the number of protein sequences between 13000 and 14000 sequences. I need to align these sequences to see the cores, the accessory and the unique sequences between these 8 proteomes. do you have a method to do this PLZ.

Four informations: I used proteinortho but I noticed that proteinortho gives only cores and accessory sequences.

Thank you in advance for your response and your help

[Joe]

If you've already got your cores and accessories, you could cluster the proteins to some identity threshold (which presumably you already did with proteinortho), using something like PSI-CD-HIT. I'm not sure how well it scales to a dataset that large, but give it a try.

Any clusters you get with only a single member are your unique proteins.

[kamel]

Excuse me, but I did not understand what you said. I used proteinortho and got a matrix (.txt file) that does not contain the unique sequences. do you have a method or tool that aligns and gives a matrix with unique, accessory and cores.

[Joe]

Not a single tool no - I am not aware of one from proteomes. Your task will probably require some scripting/coding of your own.

My suggestion is to keep the matrix you already have which gives you 2/3rds of what you asked for, and then cluster your sequences using the CD-HIT program to find unique sequences.

I don't know how else I can explain it...

Answer 1

[bioinfo17]

use the -singles option in proteinortho command