Related genomes of genome ORYRU based on shared OMA groups

How does the search work?

Input a query in the search field. Everytime you press Space or Enter after a word, a token will be created. The token is composed of a prefix describing how the query should be treated and the actual query itself.

What are the different types of tokens?

Each token represents either a Gene, HOG, OMA group, or Taxon. Prefixes are used to specify which category to associate with the query term.

Category	Prefixes
Genes	id, go, ec, description, domain, sequence
HOGs	hog, sequence
OMA Groups	omagroup, fingerprint, sequence
Taxon	species, taxid, taxon

For example, the token [go:4225] will search for genes in the OMA database annotated with the GO:0004225 gene ontology term.
How to search for a multi-word query?

If your query term is composed of multiple words (e.g homo sapiens), use " " to encapsulate it.

How many tokens can I have?

There is no limit on the number of tokens. It is not possible to enter multiple tokens of different categories, except taxon, which can be combined with other categories. For example, you can search for 'hog:60627 species:HUMAN' to return human genes found in HOG:606207.

How to edit/delete a token?

To edit a query, click on it to modify the input field. To edit a prefix, click on the dropdown icon to select another one. To remove a token, click on the x to delete it.

Autosuggest

Typing a query without hitting enter or space will prompt an autosuggestion for the identifier after a few seconds.

Search

How does the search work?

Input a query in the search field. Everytime you press Space or Enter after a word, a token will be created. The token is composed of a prefix describing how the query should be treated and the actual query itself.

What are the different types of tokens?

Each token represents either a Gene, HOG, OMA group, or Taxon. Prefixes are used to specify which category to associate with the query term.

Category	Prefixes
Genes	id, go, ec, description, domain, sequence
HOGs	hog, sequence
OMA Groups	omagroup, fingerprint, sequence
Taxon	species, taxid, taxon

For example, the token [go:4225] will search for genes in the OMA database annotated with the GO:0004225 gene ontology term.
How to search for a multi-word query?

If your query term is composed of multiple words (e.g homo sapiens), use " " to encapsulate it.

How many tokens can I have?

There is no limit on the number of tokens. It is not possible to enter multiple tokens of different categories, except taxon, which can be combined with other categories. For example, you can search for 'hog:60627 species:HUMAN' to return human genes found in HOG:606207.

How to edit/delete a token?

To edit a query, click on it to modify the input field. To edit a prefix, click on the dropdown icon to select another one. To remove a token, click on the x to delete it.

Autosuggest

Typing a query without hitting enter or space will prompt an autosuggestion for the identifier after a few seconds.

ORYRU - Oryza rufipogon

Proteome version: Ensembl Plants 23; PRJEB4137; 19-JUL-2014 with 36967 genes / 38396 proteins.

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Genome information
Chromosome viewer
List genes
Related Species

Based on number of:

Shared OMA groups

Shared HOGs
Synteny

Species with most common OMA groups

Nb.	OMA Group	Scientific Name	Nb. orthologous group
1	ORYNI	Oryza nivara	24355
2	ORYSI	Oryza sativa subsp. indica	20577
3	ORYGL	Oryza glaberrima	19045
4	WHEAT	Triticum aestivum	18750
5	ORYPU	Oryza punctata	17132
6	ORYSJ	Oryza sativa subsp. japonica	16806
7	MISSI	Miscanthus sinensis	15911
8	SETVI	Setaria viridis	15586
9	SORBI	Sorghum bicolor	14660
10	SETIT	Setaria italica	14385

Species with least common OMA groups

Nb.	OMA Group	Scientific Name	Nb. orthologous group
1	RALSL	Ralstonia solanacearum	37
2	UC116	Patescibacteria group bacterium E44_bin74	41
3	ZINIC	Zinderia insecticola (strain CARI)	43
4	MYCS3	Mycoplasma suis (strain KI_3806)	54
5	MYCHA	Mycoplasma haemolamae (strain Purdue)	54
6	UC087	Candidatus Pacebacteria bacterium LF-bin-483	54
7	UC179	candidate division Kazan bacterium GW2011_GWA1_50_15 none	55
8	MYCSL	Mycoplasma suis (strain Illinois)	57
9	MYCWM	Mycoplasma wenyonii (strain Massachusetts)	57
10	UC105	Patescibacteria group bacterium Baikal-deep-G193	59