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SynMap: Whole Genome Synteny Analysis
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:
Use all genes in target genome for analysis
Use only target genome genes that match to at least one chromosome in query genome
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?
Your E-mail Address:
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Use Org Names
Generating Pseudo Assembly
(This may take several hours)
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Questions, problems, suggestions?