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

Reference on Scoring Method

Different Gene Families in Arabidopsis thaliana Transposed in Different Epochs and at Different Frequencies throughout the Rosids

Margaret R. Woodhouse, Haibao Tang, Michael Freeling

http://www.plantcell.org/content/23/12/4241.abstract

Download Synteny Score code

https://github.com/tanghaibao/quota-alignment/blob/master/scripts/synteny_score.py