Information of genome Liliopsida

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 Liliopsida

with 24 descendant species and 52877 (15888 well supported) ancestral genes (HOGs).

‹

Common name:	Liliopsida
NCBI taxonomic identifier:	4447
Number of ancestral genes:	52877 (all HOGs) 15888 (well supported HOGs ?)
Number of ancestral genes included in ancestral contigs:	14722
Number of descendant extant species:	24

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Code	Scientific Name	Common Name	Last Update	# of Sequences	Taxon Id	D.
ZOSMR	Zostera marina	Eelgrass	2019-Sep-19	24953	29655	E
ASPOF	Asparagus officinalis	Garden asparagus	2021-Mar-15	24141	4686	E
ERATE	Eragrostis tef	Teff	2015-Dec-06	41493	110835	E
SETIT	Setaria italica	Foxtail millet	2014-Mar-02	35624	4555	E
SETVI	Setaria viridis	Green bristlegrass	2022-May-30	52459	4556	E
SORBI	Sorghum bicolor	Sorghum	2019-Apr-07	41500	4558	E
MAIZE	Zea mays	Maize	2018-Sep-16	99743	4577	E
MISSI	Miscanthus sinensis	Japanese silver grass	2022-Jun-09	89486	62337	E
ORYLO	Oryza longistaminata	Longstamen rice	2016-Jun-28	29931	4528	E
ORYRU	Oryza rufipogon	Brownbeard rice	2014-Oct-01	38396	4529	E
ORYSI	Oryza sativa subsp. indica	Rice	2014-Mar-30	40364	39946	E
ORYSJ	Oryza sativa subsp. japonica	Rice	2015-Jun-18	34225	39947	E
ORYBR	Oryza brachyantha		2014-Mar-30	31307	4533	E
ORYNI	Oryza nivara	Indian wild rice	2014-Nov-05	37747	4536	E
ORYPU	Oryza punctata	Red rice	2014-Nov-05	32361	4537	E
ORYGL	Oryza glaberrima	African rice	2013-Dec-19	31605	4538	E
BRADI	Brachypodium distachyon	Purple false brome	2014-Jan-23	26679	15368	E
HORVV	Hordeum vulgare subsp. vulgare	Domesticated barley	2018-Mar-21	194879	112509	E
WHEAT	Triticum aestivum	Wheat	2018-Aug-18	137010	4565	E
TRITD	Triticum turgidum subsp. durum	Durum wheat	2022-May-22	196105	4567	E
TRIUA	Triticum urartu	Red wild einkorn	2013-Aug-19	32635	4572	E
AEGTS	Aegilops tauschii subsp. strangulata	Goatgrass	2023-Mar-06	58655	200361	E
AEGTA	Aegilops tauschii	Tausch's goatgrass	2013-Dec-19	33795	37682	E
MUSAM	Musa acuminata subsp. malaccensis	Wild banana	2022-Jun-16	45589	214687	E

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