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TBlastX (very slow)
Relative Gene Order
We recommend using "Relative Gene Order"
Default distance settings for:
Maximum distance between two matches (-D):
Minimum number of aligned pairs (-A):
Merge Syntenic Blocks
Quota Align Merge
These settings will merge neighboring syntenic blocks. We recommend "Quota Align".
Average distance expected between syntenic blocks (-gm):
Maximum distance between two blocks (-Dm):
Ratio of coverage depth:
Window size (genes):
Restrict maximum number of chromosomes in analysis:
Max query chromosomes:
Max target chromosomes:
Skip Random/Unknown Chromosomes:
Fractionation bias calculation:
Use all genes in target genome
Use only syntenic genes in target genome (inceases fractionation signal)
Calculate syntenic CDS pairs and color dots:
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])
Regenerate dotplot images?
Show non-syntenic matches (grey dots)?
Draw boxes around syntenic regions?
Skip Random/Unknown Chromosomes?
Sort Chromosomes by:
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)
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?
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Use Org Names
Generating Pseudo Assembly
(This may take several hours)
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Questions, problems, suggestions?