Related genomes of genome TREPA 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.

TREPA - Treponema pallidum (strain Nichols)

Proteome version: 02-MAR-2010 (Rel. 118, Last updated, Version 118) with 1027 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	TREPS	Treponema pallidum subsp. pallidum (strain SS14)	982
2	TREPM	Treponema pallidum subsp. pertenue (strain Samoa D)	935
3	TREPD	Treponema pallidum subsp. pertenue (strain CDC2)	934
4	TREPU	Treponema paraluiscuniculi (strain Cuniculi A)	877
5	TREPC	Treponema pallidum subsp. pallidum (strain Chicago)	854
6	TREDE	Treponema denticola (strain ATCC 35405 / DSM 14222 / CIP 103919 / JCM 8153 / KCTC 15104)	635
7	TRECH	Treponema caldarium (strain ATCC 51460 / DSM 7334 / H1)	572
8	TREBD	Treponema brennaborense (strain DSM 12168 / CIP 105900 / DD5/3)	572
9	SEDSS	Sediminispirochaeta smaragdinae (strain DSM 11293 / JCM 15392 / SEBR 4228)	563
10	TREAZ	Treponema azotonutricium (strain ATCC BAA-888 / DSM 13862 / ZAS-9)	539

Species with least common OMA groups

Nb.	OMA Group	Scientific Name	Nb. orthologous group
1	TRYCI	Trypanosoma congolense (strain IL3000)	6
2	MONPE	Moniliophthora perniciosa (strain FA553 / isolate CP02)	12
3	MEGSC	Megaselia scalaris	16
4	VITCO	Vittaforma corneae (strain ATCC 50505)	17
5	ENTBH	Enterocytozoon bieneusi (strain H348)	18
6	NANGC	Nannochloropsis gaditana (strain CCMP526)	18
7	TRAHO	Trachipleistophora hominis	18
8	SYMMI	Symbiodinium microadriaticum	18
9	POSPM	Postia placenta (strain ATCC 44394 / Madison 698-R)	20
10	NANST	Nanobsidianus stetteri	21