Related genomes of genome VARPS 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.

VARPS - Variovorax paradoxus (strain S110)

Proteome version: 13-AUG-2009 (Rel. 101, Last updated, Version 2) with 6272 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	VARPE	Variovorax paradoxus (strain EPS)	3943
2	CUPNN	Cupriavidus necator (strain ATCC 43291 / DSM 13513 / CCUG 52238 / LMG 8453 / N-1)	2617
3	DELAS	Delftia acidovorans (strain DSM 14801 / SPH-1)	2593
4	DELSC	Delftia sp. (strain Cs1-4)	2582
5	POLSJ	Polaromonas sp. (strain JS666 / ATCC BAA-500)	2550
6	CUPNH	Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337)	2482
7	PARXL	Paraburkholderia xenovorans (strain LB400)	2423
8	ACIAP	Acidovorax avenae (strain ATCC 19860 / DSM 7227 / CCUG 15838 / JCM 20985 / LMG 2117 / NCPPB 1011)	2419
9	CUPPJ	Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197)	2384
10	BURCH	Burkholderia cenocepacia (strain HI2424)	2331

Species with least common OMA groups

Nb.	OMA Group	Scientific Name	Nb. orthologous group
1	VITCO	Vittaforma corneae (strain ATCC 50505)	17
2	ENTBH	Enterocytozoon bieneusi (strain H348)	20
3	TRAHO	Trachipleistophora hominis	22
4	EDHAE	Edhazardia aedis (strain USNM 41457)	24
5	NEMP3	Nematocida parisii (strain ERTm3)	26
6	NEMS1	Nematocida sp. 1 (strain ERTm2 / ATCC PRA-371)	28
7	VAVCU	Vavraia culicis (isolate floridensis)	29
8	UC149	Candidatus Huberarchaeum crystalense CG_4_9_14_0_8_um_filter_31_21	31
9	NOSCE	Nosema ceranae (strain BRL01)	32
10	SPRLO	Spraguea lophii (strain 42_110)	33