SynFind

Overview

SynFind identified syntenic regions against any set of genomes given a gene in one genome. The primary algorithm of this analysis is SyntenyScore written by Haibao Tang.

Options for Synteny Score

• Window Size: synteny window size in genes [default: 40]
  • The Window Size is the size of the genomic regions compared between two genomes using genes as the metric. Given an anchor gene, the window size is divided by 2 and that many genes searched up and downstream from the anchor.
  • Example, a window size of 40 means that a total of 41 genes are checked: the anchor gene; plus 20 upstream; plus 20 downstream.
• Cutoff: the minimum number of anchors to call synteny. This is a percentage of the total number of genes in a window. [default: 0.1]
  • Valid value range: (0,1]
  • Example: Window size of 40; cutoff value of 0.1: 4 gene-pairs must be identified for a region to be called syntenic.
• Scoring Function: scoring scheme, must be one of ('collinear', 'density') [default: collinear]
  • Collinear: a collinear arrangement of syntenic genes in enforced
  • Density: any arrangement of gene-pairs is tolerated