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:

1. 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.
2. 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.