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==Options for Synteny Score== | ==Options for Synteny Score== | ||
* '''Window Size''': synteny window size [default: 40] | * '''Window Size''': synteny window size in genes [default: 40] | ||
* '''Cutoff''': the minimum number of anchors to call synteny [default: 0.1] | ** 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] | * '''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 | |||
Revision as of 00:29, 5 February 2012
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