I have a little example  fasta file with protein fragments to figure out how usearch works:

fragments

    >seq1
    TKEHALSKERAA
    
    >seq2
    KKEHALSKERAR
    
    >seq3
    AAHAASAERAAE
    
    >seq4
    AAHAASAERAAS

I used usearch with the following options:

    usearch -cluster_fast  ex.fasta -id  0.5 -uc cluster.uc

I expect at most 2 clusters (1,2) and (3,4) but the result contains only singletons.I decreased the identity and also the gap penalties but the result is the same.

Any idea?

Thank You


I think your sequences are too short. Try reducing the `-minhsp` value, but it simply may not work with these sequence lengths. If you duplicate each sequence and make the length 24 instead of 12, you will get the desired clusters.