Blasting an unknown protein with a predicted pattern

ahmadkhalifa · 04-21-2019, 10:23 PM

Hello,

I want to blast a certain pattern that I think exist in my protein. I know the organism where the protein is expressed, but I don't know the identity or the sequence of the protein. I also have an idea about the total length of the protein and where my pattern of interest might lie.

I looked into phi-blast but it requires that I provide a sequence! Can I provide a sequence made up of wild cards corresponding to the length of my protein? How to restrict the pattern searching to a certain location in the sequence?

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04-21-2019, 10:23 PM	#1
ahmadkhalifa Junior Member Location: Montreal Join Date: Apr 2019 Posts: 1	Blasting an unknown protein with a predicted pattern Hello, I want to blast a certain pattern that I think exist in my protein. I know the organism where the protein is expressed, but I don't know the identity or the sequence of the protein. I also have an idea about the total length of the protein and where my pattern of interest might lie. I looked into phi-blast but it requires that I provide a sequence! Can I provide a sequence made up of wild cards corresponding to the length of my protein? How to restrict the pattern searching to a certain location in the sequence?