How to reduce the redundance in proteomic dataset
Hello, I am working with several sets of proteomics, one of the steps I need is to reduce redundancy to be able to move on to the next analyses. However, I wanted to know what software to use on Windows, I have seen that there is cd-hit, does anyone have experience with that?
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Not for Windows (unless you can use WSL2 on Win 11)
MMSeqs2(LINK) is likely the current state of the art for clustering at this time.This paper describes a pipeline that UniProt uses for their proteomes but it does not appear to be accessible for end-users directly: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5199198/