CoGe: SynMap

Organism 1 Search:

Name: Description:

Organism count: 1

Genome:

Organism: Arabidopsis lyrata

Description:Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis

Genome Information:

Source:	JGI
Dataset:	Araly1_assembly_scaffolds.fasta
Chromosome count:	695
DNA content:	Click to retrieve
Total length:	206,667,935
Contains contigs

Organism 2 Search:

Name: Description:

Organism count: 1

Genome:

Organism: Arabidopsis thaliana Col-0 (thale cress)

Genome Information:

Source:	TAIR
Dataset:	ch2.xml: TAIR Version 8 Chromosome 2, TIGR XML format
Chromosome count:	5
DNA content:	Click to retrieve
Total length:	119,186,497

Blast Algorithm:

DAGChainer Options:

Relative Gene Order Nucleotide DistanceWe 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:

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)?

E-mail results?