CoGe: SynMap

Would you like to log out of all CyVerse applications?

Log out of CoGe only Log out of all CyVerse services

CoGe
- advanced
  
  Type
  
  Any Genomes Organisms Features Experiments Notebooks
  
  Refine
  
  Tag
  
  Feature type
  
  Metadata =
  
  Certified
  
  Clear all Search

My Data
Tools
- OrganismView
- CoGeBlast
- FeatView
- SynFind
- SynMap
- SynMap3D
- GEvo
- Load Genome
- LoadExp+
- Taxonomy
Help
- CoGePedia
- Page Docs
- Forums
- FAQ
- Tutorials
- Cite CoGe
- System Support
Log in
- Log in with CAS

SynMap generates a syntenic dotplot between two organisms and identifies syntenic regions. More...

Finds putative genes or regions of homology between two genomes
Identies collinear sets of genes or regions of sequence similarity to infer synteny
Generates a dotplot of the results and coloring syntenic pairs.

If you choose, synonymous and non-synonymous site mutation data can be calculated for protein coding genes that are identified as syntenic. These genes will then be colored based on those values in the dotplot for rapid identification of different age-classes of syntenic regions.

Click here for an example analysis between Arabidopsis thaliana and Arabidopsis lyrata.

Click here for an explanation of the results.

Select Organisms
Analysis Options
Display Options

Need help?

Organism 1

Organism 2

Blast Algorithm

DAGChainer Options

Relative Gene Order Nucleotide Distance We recommend using "Relative Gene Order"
Default distance settings for:
Maximum distance between two matches (-D):
Minimum number of aligned pairs (-A): genes

Merge Syntenic Blocks Algorithm: These settings will merge neighboring syntenic blocks. We recommend "Quota Align".

Average distance expected between syntenic blocks (-gm):
Maximum distance between two blocks (-Dm):

Syntenic Depth

Algorithm:
Ratio of coverage depth: -to-
Overlap distance:

Fractionation Bias

Run:
Window size (genes):
Restrict maximum number of chromosomes in analysis:
Max query chromosomes:
Max target chromosomes:
Skip Random/Unknown Chromosomes:
Use all genes in target genome
Use only syntenic genes in target genome (inceases fractionation signal)

CodeML

Calculate syntenic CDS pairs and color dots: substitution rates SLOW
Color scheme:
Min Val: Max Val: Log10 Transform:
Only applicable to protein coding sequences (CDS vs. CDS)

Advanced Options ( see page docs)

Tandem duplication distance
C-score (filters low quality hits: value [0-1]) 0
Force regenerate analysis Check this to completely regenerate the analysis, ignoring any cached results

Visualizer Select

SynMap2 Legacy Version Use legacy version if your previous analysis froze.

SynMap2 options

Syntenic Path Assembly (SPA)?

Legacy options

Regenerate dotplot images?
Show non-syntenic matches (grey dots)?
Draw boxes around syntenic regions?
Label Chromosomes?
Skip Random/Unknown Chromosomes?
Sort Chromosomes by:
Flip axes?
Color diagonals by: Synonymous rates will supercede this option.
Dotplot axis metric:
Dotplot axes relationship:
Master image width (0 == dynamic)
Minimum chromosome size:
Syntenic Path Assembly (SPA)?
Options: Reference genome (to which the other genome is assembled) has pieces (contigs, scaffolds, etc)
(Note: SPA is not compatible with syntenic depth or merging syntenic blocks. If SPA is selected with those options, your dotplot image will fail to be drawn.)
Hide contigs without synteny?
Your E-mail Address:
Job Title: Use Org Names

Generate SynMap

Generating Pseudo Assembly

(This may take several hours)

Please wait ...

An error occurred
Close

Finished!
OK

Please wait ...

Questions, problems, suggestions? Contact us or Ask CyVerse