Difference between revisions of "SynFind"
From CoGepedia
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[[SynFind Syntenic Depth Examples]] | [[SynFind Syntenic Depth Examples]] | ||
| − | ==Options for Synteny | + | ==Options for SynFind== |
| − | * ''' | + | |
| + | ===General parameters=== | ||
| + | *Comparison algorithm: Select the algorithm for comparing genomes. We recommend Last! Much, much faster than LastZ! | ||
| + | |||
| + | ===Synteny Finding: SyntenyScore=== | ||
| + | SynFind is powered by SyntenyScore (part of the BaoTools Package): | ||
| + | *Full github repo: https://github.com/tanghaibao | ||
| + | *Package with SyntenyScore: https://github.com/tanghaibao/quota-alignment | ||
| + | |||
| + | ===Parameters=== | ||
| + | * '''Gene 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. | ** 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. | ** Example, a window size of 40 means that a total of 41 genes are checked: the anchor gene; plus 20 upstream; plus 20 downstream. | ||
| − | * ''' | + | * '''Minimum number of genes''': The minimum number of anchoring genes to call a region syntenic. [default: 4] |
| − | + | ||
| − | + | ||
* '''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 | ** Collinear: a collinear arrangement of syntenic genes in enforced | ||
Revision as of 14:33, 23 May 2012
Contents
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.
Syntenic Depth
SynFind calculates the number and percentage of genes for a particular Syntenic depth in each target genome.
SynFind Syntenic Depth Examples
Options for SynFind
General parameters
- Comparison algorithm: Select the algorithm for comparing genomes. We recommend Last! Much, much faster than LastZ!
Synteny Finding: SyntenyScore
SynFind is powered by SyntenyScore (part of the BaoTools Package):
- Full github repo: https://github.com/tanghaibao
- Package with SyntenyScore: https://github.com/tanghaibao/quota-alignment
Parameters
- Gene 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.
- Minimum number of genes: The minimum number of anchoring genes to call a region syntenic. [default: 4]
- 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
