Synteny Block
Definition
A synteny block is a region of closely related genes. They are helpful in genome rearrangement, to determine genomic similarities between two genomes from different species.
Construction
Two compare the genomes of two organisms, one can first:
- Construct shared-kmer dot-plots between the two. For genomes $A$ and $B$, $SharedKmer^k_{i, j} = 1(Kmer(A, i, k) = Kmer(B, j, k))$, taking reverse-complement pairings into account.
- Find diagonals of $SharedKmer^k$ greater than a certain length (to remove noise). The sign of the synteny block is based on the strandedness of the match: positive means a $5’ \to 3’$ and negative means $3’\to 5’$ (reverse complement). To find the diagnonals, one can use simple techniques like connected components of a graph consisting of shared-kmers within a certain max-distance of each other.