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Hi
I have a set of proteins and would like to remove any isoforms if present, so I only keep the longest splice variant of each gene in my dataset. I'm currently trying to use all-vs-all blastp to accomplish this, but I was wondering whether this is the most optimal way?
In the literature I have looked at it seems like a very straight forward analysis, but I've only seen references to custom perl scripts or it is simply stated that only the longest isoforms were used in subsequent analyses.
Oh, I should point out the sequences I'm working with are from a non-model organism.
any help or suggestions are highly appreciated.
I have a set of proteins and would like to remove any isoforms if present, so I only keep the longest splice variant of each gene in my dataset. I'm currently trying to use all-vs-all blastp to accomplish this, but I was wondering whether this is the most optimal way?
In the literature I have looked at it seems like a very straight forward analysis, but I've only seen references to custom perl scripts or it is simply stated that only the longest isoforms were used in subsequent analyses.
Oh, I should point out the sequences I'm working with are from a non-model organism.
any help or suggestions are highly appreciated.
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