Whole Genome Synteny
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SynMap is a very computationally intense, multi-step program which may take hours to complete for large genomes.
If available, select previously run parameter-sets for your organisms to see results instantly. Get Started: Click here for an example analysis between Arabidopsis thaliana and Arabidopsis lyrata. (Note that syntenic gene pairs are colored by synonymous mutations (Ks))Click here for an explaination of the results. |
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Organism 1 Search:
Name:
Description:
Organism count: 15094
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Organism 2 Search:
Name:
Description:
Organism count: 15094
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| Blast Algorithm: | |||||||
| DAGChainer Options: |
We recommend using "Relative Gene Order"
Default distance settings for:
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| Merge Syntenic Blocks: |
Algorithm:
These settings will merge neighboring syntenic blocks. We recommend "Quota Align".
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| Syntenic Depth | Algorithm:
Ratio of coverage depth:
-to-
Overlap distance: | ||||||
| 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 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? | |||||||
| 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: E-mail results?
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