Related genomes of genome ORYSJ 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.

ORYSJ - Oryza sativa subsp. japonica

Proteome version: Ensembl Plants 27; IRGSP-1; 26-MAY-2015 with 33090 genes / 34225 proteins.

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Genome information
List genes
Related Species

Based on number of:

Shared OMA groups

Shared HOGs
Gene Order
Synteny

Species with most common OMA groups

Nb.	OMA Group	Scientific Name	Nb. orthologous group
1	ORYSI	Oryza sativa subsp. indica	18446
2	WHEAT	Triticum aestivum	18244
3	ORYGL	Oryza glaberrima	17302
4	ORYRU	Oryza rufipogon	17002
5	ORYNI	Oryza nivara	16801
6	MISSI	Miscanthus sinensis	15554
7	SETVI	Setaria viridis	14968
8	ORYPU	Oryza punctata	14615
9	SORBI	Sorghum bicolor	14018
10	SETIT	Setaria italica	13788

Species with least common OMA groups

Nb.	OMA Group	Scientific Name	Nb. orthologous group
1	RALSL	Ralstonia solanacearum	37
2	ZINIC	Zinderia insecticola (strain CARI)	38
3	UC116	Patescibacteria group bacterium E44_bin74	42
4	MYCHA	Mycoplasma haemolamae (strain Purdue)	47
5	TRYVY	Trypanosoma vivax (strain Y486)	47
6	MYCS3	Mycoplasma suis (strain KI_3806)	50
7	MYCWM	Mycoplasma wenyonii (strain Massachusetts)	50
8	MYCSL	Mycoplasma suis (strain Illinois)	53
9	UC179	candidate division Kazan bacterium GW2011_GWA1_50_15 none	54
10	UC087	Candidatus Pacebacteria bacterium LF-bin-483	55