Related genomes of genome ALIFM 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.

ALIFM - Aliivibrio fischeri (strain MJ11)

Proteome version: 16-DEC-2008 (Rel. 100, Last updated, Version 2) with 4034 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	ALIF1	Aliivibrio fischeri (strain ATCC 700601 / ES114)	3270
2	ALISL	Aliivibrio salmonicida (strain LFI1238)	2681
3	VIBPA	Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)	2526
4	VIBA3	Vibrio atlanticus (strain LGP32)	2511
5	VIBCB	Vibrio campbellii (strain ATCC BAA-1116 / BB120)	2484
6	VIBAE	Vibrio antiquarius (strain Ex25)	2482
7	VIBVY	Vibrio vulnificus (strain YJ016)	2480
8	VIBVM	Vibrio vulnificus (strain MO6-24/O)	2460
9	VIBVU	Vibrio vulnificus (strain CMCP6)	2428
10	VIBSN	Vibrio sp. (strain N418)	2394

Species with least common OMA groups

Nb.	OMA Group	Scientific Name	Nb. orthologous group
1	TRYVY	Trypanosoma vivax (strain Y486)	4
2	VITCO	Vittaforma corneae (strain ATCC 50505)	20
3	ENTBH	Enterocytozoon bieneusi (strain H348)	23
4	EDHAE	Edhazardia aedis (strain USNM 41457)	28
5	TRAHO	Trachipleistophora hominis	30
6	NEMP3	Nematocida parisii (strain ERTm3)	32
7	MONPE	Moniliophthora perniciosa (strain FA553 / isolate CP02)	32
8	TRYCI	Trypanosoma congolense (strain IL3000)	33
9	UC149	Candidatus Huberarchaeum crystalense CG_4_9_14_0_8_um_filter_31_21	33
10	NEMS1	Nematocida sp. 1 (strain ERTm2 / ATCC PRA-371)	34