CoGe: SynMap

New CoGe: Version 4! Read more
(Powered by iPlant)

Whole Genome Synteny

Please Note:

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.

Organism 1 Search:

Name: Description:

Organism count: 12913

Genome:

Organism 2 Search:

Name: Description:

Organism count: 12913

Genome:

Blast Algorithm:

Filter Repetitive Matches:

Expected number of hits per sequence

DAGChainer Options:

Relative Gene Order Nucleotide DistanceWe recommend using "Relative Gene Order" Default distance settings for:


Average distance expected between syntenic genes (-g):
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:

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)

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:

Order contigs by best syntenic path?

E-mail results?

Date: 2012-02-08 21:52:34