Related genomes of genome PHYPA 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.

PHYPA - Physcomitrium patens

Proteome version: Ensembl Plants 21; ASM242v1; 4-DEC-2013 with 31841 genes / 32775 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	WHEAT	Triticum aestivum	8528
2	BRANA	Brassica napus	8002
3	GOSHI	Gossypium hirsutum	7744
4	TOBAC	Nicotiana tabacum	6867
5	SOYBN	Glycine max	6793
6	MISSI	Miscanthus sinensis	6298
7	SELML	Selaginella moellendorffii	6224
8	TRITD	Triticum turgidum subsp. durum	5939
9	ACTCC	Actinidia chinensis var. chinensis	5773
10	MUSAM	Musa acuminata subsp. malaccensis	5768

Species with least common OMA groups

Nb.	OMA Group	Scientific Name	Nb. orthologous group
1	RALSL	Ralstonia solanacearum	35
2	MYCHA	Mycoplasma haemolamae (strain Purdue)	47
3	ZINIC	Zinderia insecticola (strain CARI)	47
4	MYCWM	Mycoplasma wenyonii (strain Massachusetts)	47
5	TRYVY	Trypanosoma vivax (strain Y486)	49
6	UC116	Patescibacteria group bacterium E44_bin74	51
7	UC087	Candidatus Pacebacteria bacterium LF-bin-483	53
8	MYCS3	Mycoplasma suis (strain KI_3806)	53
9	MYCSL	Mycoplasma suis (strain Illinois)	56
10	MYCHN	Mycoplasma haemocanis (strain Illinois)	61