Information of genome Passeriformes

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 Passeriformes

with 7 descendant species and 21873 (16252 well supported) ancestral genes (HOGs).

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Common name:	Passeriformes
NCBI taxonomic identifier:	9126
Number of ancestral genes:	21873 (all HOGs) 16252 (well supported HOGs ?)
Number of ancestral genes included in ancestral contigs:	15570
Number of descendant extant species:	7

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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

Showing 1 to 7 of 7 rows