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  • Cluster complete plasmid sequences

    Hey all,
    I have complete nucleotide sequences for 119 plasmids, with sizes ranging from 500 to 170000 base pairs. Is there a way to cluster those sequences such that I can sort out sequence redundancy? (for example, if a small sequence is covered to 100% in one of the bigger sequences, I want to recognize that in the cluster)

    I have tried doing it in uclust, but I think it cannot manage the length of the sequences.
    Can anyone recommend a good tool to do this?

    Thank you!

  • #2
    For reference cross-posted: https://www.biostars.org/p/181585

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