Synteny Analysis
The synteny analysis tool performs pairwise comparison of gene orders on the chromosome by the genome alignment method and reports all instances of locally similar gene orders, which may be considered as conserved synteny.
The gene order is treated as a sequence of KO identifiers (K numbers). The query data must consist of two columns, gene identifiers in the first column and assigned K numbers in the second column, which are ordered according to the chromosomal positions. This data format is consistent with the outputs of automatic annotation servers: BlastKOALA and GhostKOALA.
The gene order is treated as a sequence of KO identifiers (K numbers). The query data must consist of two columns, gene identifiers in the first column and assigned K numbers in the second column, which are ordered according to the chromosomal positions. This data format is consistent with the outputs of automatic annotation servers: BlastKOALA and GhostKOALA.
Usage
Query data
The query dataset is an ordered list of genes along the chromosome that are annotated with K numbers. It must be prepared as a tab-delimited two-column dataset with the user's gene identifiers in the first column and assigned K numbers in the second column. This is consistent with the output files of automatic annotation servers: BlastKOALA and GhostKOALA.
Genome ID
Genome ID may be KEGG organism code or vtax number (virus taxonomy ID). Use the "Find similar KEGG organisms" button to obtain cadidates of genomes to be compared according to the KO composiition similarity.
Last updated: December 10, 2025