I have downloaded a dataset of 2086 proteins from RCSB with certain criteria. I want to remove redundant protein sequences. My aim is to remove the PDB IDs that have almost same protein sequences(having only two or three mutations) . Please help me if anyone knows how to do it.
Related to your query, I suggest you to follow this thread of answers/discussion: https://www.researchgate.net/post/How_can_I_remove_redundancy_in_sequence_data_sets
Also : https://star-protocols.cell.com/protocols/1439
https://www.uniprot.org/help/proteome_redundancy
Incorrect description of the question.
Removing redundancy is not the same as clustering sequences.
And clustering sequences with 25% identity does not make any logical sense.
When we download thousands of sequences for databases, we often pick multiple copies of the same sequences which are submitted by different group or sometimes different strains. I want to remove the PDB ID s that have almost same protein sequences (having only two or three mutations)..
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