CoGe: SynMap

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Organism 1:

Organisms: (1)

Genomes:

Description:	Escherichia coli K12 strain K-12 substrain MG1655 (v2, id4242): unmasked
Taxonomy:	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Escherichia
Source:	CoGe Certified Genome
Dataset:	7122-structural-annotations.gff
Chromosomes:	1
DNA content:	GC: 50.79%, AT: 49.21%, N: 0%, X: 0%
Total length:	4,639,675

Organism 2:

Organisms: (1)

Genomes:
No Coding Sequence in Genome

Description:	Escherichia coli K12 strain K-12 substrain NCM4370 (v.2, id6874): unmasked
Taxonomy:	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Escherichia
Source:	Kustu Laboratory
Dataset:	mid5_denovo_454AllContigs.fna: de novo assembly by Roche using Newbler
Chromosomes:	144
DNA content:	Click to retrieve
Total length:	4,655,361
Contains contigs

Blast Algorithm

DAGChainer Options

Relative Gene Order Nucleotide Distance We 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".

Syntenic Depth

Fractionation Bias

Run:
Window size (genes):
Restrict maximum number of chromosomes in analysis:
Max query chromosomes:
Max target chromosomes:
Skip Random/Unknown Chromosomes:
Use all genes in target genome
Use only syntenic genes in target genome (inceases fractionation signal)

CodeML

Advanced Options ( see page docs)

Visualizer Select

SynMap2 options

Legacy options

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: 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:
Job Title: Use Org Names