Information of genome Neognathae

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 Neognathae

with 18 descendant species and 28913 ancestral genes (HOGs).

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Common name:	Neognathae
NCBI taxonomic identifier:	8825
Number of ancestral genes:	28913
Number of descendant extant species:	18

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Code	Scientific Name	Common Name	Last Update	# of Sequences	Taxon Id	D.
PARMJ	Parus major	Great tit	2019-Jun-18	26297	9157	E
JUNHY	Junco hyemalis	Dark-eyed junco	2019-Sep-18	22418	40217	E
FICAL	Ficedula albicollis	Collared flycatcher	2013-Oct-03	15383	59894	E
SERCA	Serinus canaria	Island canary	2019-Jun-18	23606	9135	E
CHLGU	Chloebia gouldiae	Gouldian finch	2021-Apr-28	23847	44316	E
TAEGU	Taeniopygia guttata	Zebra finch	2022-Jun-19	32098	59729	E
CORMO	Corvus moneduloides	New Caledonian crow	2022-Aug-30	28454	1196302	E
MELUD	Melopsittacus undulatus	Budgerigar	2019-Sep-19	21972	13146	E
STRHB	Strigops habroptila	Kakapo	2021-Apr-28	24520	2489341	E
TYTAL	Tyto alba	Barn owl	2022-Aug-31	41980	56313	E
ATHCN	Athene cunicularia	Burrowing owl	2021-Jun-22	22665	194338	E
HALLE	Haliaeetus leucocephalus	Bald eagle	2022-Aug-31	25265	52644	E
FALTI	Falco tinnunculus	Common kestrel	2022-Aug-29	25330	100819	E
ANAPP	Anas platyrhynchos platyrhynchos	Northern mallard	2020-Nov-01	27833	8840	E
ANAPL	Anas platyrhynchos	Domestic duck	2013-Oct-03	15753	8839	E
CHICK	Gallus gallus	Chicken	2023-May-01	68684	9031	E
PHACC	Phasianus colchicus	Common pheasant	2021-Jul-18	25525	9054	E
MELGA	Meleagris gallopavo	Common turkey	2013-Mar-05	14627	9103	E

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