CoGe: SynMap

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Organism 1:

Organisms: (1)

Genomes:

Description:	Sorghum bicolor (v1.4, id93): unmasked
Taxonomy:	Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Liliopsida; commelinids; Poales; Poaceae; PACCAD clade; Panicoideae; Andropogoneae; Sorghum
Source:	JGI
Dataset:	Sorbi1_assembly_scaffolds.fasta: Sorghum sequence
Chromosomes:	3,304
DNA content:	Click to retrieve
Total length:	738,540,932
Contains contigs

Organism 2:

Organisms: (1)

Genomes:

Description:	Zea mays (maize; corn) (refgen_v2 assembly (working gene set annotations: 5a)) (v2, id9106): unmasked
Taxonomy:	Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Liliopsida; commelinids; Poales; Poaceae; PACCAD clade; Panicoideae; Andropogoneae; Zea; Zea mays
Name:	refgen_v2 assembly (working gene set annotations: 5a)
Source:	MaizeSequence.org
Dataset:	maize_pseudo_v2.tar.gz: B73 refgen_v2 assembly
Chromosomes:	11
DNA content:	Click to retrieve
Total length:	2,065,722,704

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