Entering edit mode
3.4 years ago
g.papp-co
▴
30
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