I have a set of 2000 sequences. In that set there are two sequences
>Seq1
AAAAAAAAAAAAAAAAAAAAAAA
>Seq2
UUUUUUUUUUUUUUUUUUUUU
When clustering with Cd-hit-est with default options, these two are put in same cluster with Seq1 as representative and Seq2 as.... -/100%
Is this correct?
Angana Ray Yep, you are accurate. Cd-hit-est employs a word counting method to group sequences with a high degree of similarity depending on a user-specified identity threshold. The identity criterion is set to 90% by default, which indicates that sequences with 90% or higher similarity will be grouped together. In your example, Seq1 and Seq2 have no nucleotide sequence similarity, thus they are clustered together as a singleton cluster with Seq1 as the "typical" sequence and a similarity score of -/100%. This score denotes that the sequence bears no resemblance to any other sequence in the cluster.
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