Synteny for genome STAAM

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?

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?

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.

STAAM - Staphylococcus aureus (strain Mu50 / ATCC 700699)

Proteome version: 02-MAR-2010 (Rel. 118, Last updated, Version 118) with 2715 proteins.

Select a Tab

‹

Genome information
Chromosome viewer
List genes
Related Species

Based on number of:

Shared OMA groups

Shared HOGs
Synteny

Genome 1

Enter second genome name:
Example: HUMAN or Homo sapiens

Synteny viewer of the chromosome versus chromosome

Welcome to the synteny viewer

If you want to visualise the synteny of Staphylococcus aureus (strain Mu50 / ATCC 700699) genome with an other genome you need to first select a second genome in the left sidebar.

Then, a chromosome selection widget will open and guide you to configure the viewer !

STAAM - Staphylococcus aureus (strain Mu50 / ATCC 700699)

Based on number of:

Synteny viewer of the chromosome versus chromosome

Welcome to the synteny viewer

History

Versions

Time

Settings from 'pybrowser_dev.settings.profiling'

Headers

Request

SQL queries from 0 connections

Static files (0 found, 17 used)

Templates (7 rendered)

Alerts

Cache calls from 1 backend

Signals

Community

STAAM - Staphylococcus aureus (strain Mu50 / ATCC 700699)

Based on number of:

Synteny viewer of the chromosome versus chromosome

Action for rectangle selection

Type of relations visible

Welcome to the synteny viewer ×

History

Versions

Time

Settings from 'pybrowser_dev.settings.profiling'

Headers

Request

SQL queries from 0 connections

Static files (0 found, 17 used)

Templates (7 rendered)

Alerts

Cache calls from 1 backend

Signals

Community

Welcome to the synteny viewer