Information of genome Rodentia

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.

Ancestral genome of Rodentia

with 13 descendant species and 34114 (20081 well supported) ancestral genes (HOGs).

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Common name:	Rodentia
NCBI taxonomic identifier:	9989
Number of ancestral genes:	34114 (all HOGs) 20081 (well supported HOGs ?)
Number of ancestral genes included in ancestral contigs:	19429
Number of descendant extant species:	13

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Code	Scientific Name	Common Name	Last Update	# of Sequences	Taxon Id	D.
DIPOR	Dipodomys ordii	Ord's kangaroo rat	2022-Jun-19	23962	10020	E
CAVPO	Cavia porcellus	Guinea pig	2022-Jun-19	25582	10141	E
CAVAP	Cavia aperea	Brazilian guinea pig	2018-Nov-21	18698	37548	E
OCTDE	Octodon degus	Degu	2017-Aug-23	27047	10160	E
HETGA	Heterocephalus glaber	Naked mole rat	2018-Dec-29	28099	10181	E
FUKDA	Fukomys damarensis	Damaraland mole rat	2018-Jan-28	23339	885580	E
CHILA	Chinchilla lanigera	Long-tailed chinchilla	2017-Nov-08	25278	34839	E
ICTTR	Ictidomys tridecemlineatus	Squirrel	2012-Jul-02	19039	43179	E
JACJA	Jaculus jaculus	Lesser Egyptian jerboa	2017-Nov-29	25180	51337	E
CRIGR	Cricetulus griseus	Chinese hamster	2018-Nov-05	26985	10029	E
MOUSE	Mus musculus	Mouse	2021-Sep-16	67158	10090	E
RATNO	Rattus norvegicus	Rat	2022-Jun-19	45936	10116	E
NANGA	Nannospalax galili	Northern Israeli blind subterranean mole rat	2017-Nov-08	26869	1026970	E

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