BOL

Unique k-mers and distinct k-mers are related concepts in bioinformatics, specifically in the context of analyzing DNA or RNA sequences.

• Unique k-mers: These are k-mers (short sequences of DNA or RNA of length k) that occur only once in a given set of sequences. Unique k-mers can be useful for genome assembly, error correction, and identifying novel sequences.

• Distinct k-mers: These are k-mers that are unique within a single sequence, but may occur multiple times in a set of sequences. Distinct k-mers can be useful for quantifying the abundance or expression of different sequences within a sample.

To give an example, suppose we have a set of three DNA sequences:

If we consider k-mers of length 4 (4-mers), we can identify the unique and distinct k-mers:

• Unique 4-mers: ATGC, TGCN, GCAT, CATG, CGCA, GCAG, AGCG, GCGC, CGCG, GCGT, CGTA, GTAC, TACG, ACGT, CGTG, GTGT
• Distinct 4-mers: ATGC, TGCN, GCAT, CATG, CGCG, GCAG, AGCG, GCGC, GCGT, CGTA, GTAC, TACG, ACGT, CGTG, GTGT

Note that the k-mer "TGCN" is a unique 4-mer because it only appears once in the set of sequences, while the k-mer "CGCG" is a distinct 4-mer because it appears twice (once in Seq2 and once in Seq3), but is unique within each sequence.