rest.ensemblgenomes.org rest.ensemblgenomes.org

rest.ensemblgenomes.org

Ensembl Rest API - Ensembl Genomes REST API Endpoints

About the Ensembl Project. Ensembl Genomes REST API Endpoints. Uses the given identifier to return the archived sequence. Retrieve the archived sequence for a set of identifiers. Retrieves gene family information by ID. Retrieves gene families to which a gene belongs. Retrieves gene families to which a gene belongs. Retrieves a gene tree dump for a gene tree stable identifier. Retrieves a gene tree that contains the stable identifier. Retrieves a gene tree containing the gene identified by a symbol.

http://rest.ensemblgenomes.org/

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Ensembl Rest API - Ensembl Genomes REST API Endpoints | rest.ensemblgenomes.org Reviews
<META>
DESCRIPTION
About the Ensembl Project. Ensembl Genomes REST API Endpoints. Uses the given identifier to return the archived sequence. Retrieve the archived sequence for a set of identifiers. Retrieves gene family information by ID. Retrieves gene families to which a gene belongs. Retrieves gene families to which a gene belongs. Retrieves a gene tree dump for a gene tree stable identifier. Retrieves a gene tree that contains the stable identifier. Retrieves a gene tree containing the gene identified by a symbol.
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KEYWORDS
1 endpoints
2 user guide
3 change log
4 contact ensembl
5 archive
6 resource
7 get archive/id/ id
8 post archive/id
9 comparative genomics
10 get family/id/ id
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endpoints,user guide,change log,contact ensembl,archive,resource,get archive/id/ id,post archive/id,comparative genomics,get family/id/ id,get family/member/id/ id,get genetree/id/ id,get genetree/member/id/ id,get alignment/region/ species/ region,lookup
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Ensembl Rest API - Ensembl Genomes REST API Endpoints | rest.ensemblgenomes.org Reviews

https://rest.ensemblgenomes.org

About the Ensembl Project. Ensembl Genomes REST API Endpoints. Uses the given identifier to return the archived sequence. Retrieve the archived sequence for a set of identifiers. Retrieves gene family information by ID. Retrieves gene families to which a gene belongs. Retrieves gene families to which a gene belongs. Retrieves a gene tree dump for a gene tree stable identifier. Retrieves a gene tree that contains the stable identifier. Retrieves a gene tree containing the gene identified by a symbol.

INTERNAL PAGES

rest.ensemblgenomes.org rest.ensemblgenomes.org
1

Ensembl Genomes REST API - GET genetree/member/id/:id

http://rest.ensemblgenomes.org/documentation/info/genetree_member_id

About the Ensembl Genomes Project. Retrieves a gene tree that contains the stable identifier. An Ensembl stable ID. Return the aligned string if true. Otherwise, return the original sequence (no insertions). Name of the callback subroutine to be returned by the requested JSONP response. Required ONLY when using JSONP as the serialisation method. Please see the user guide. Return the aligned sequence encoded in CIGAR format. The format of a NH (New Hampshire) request. Filter by feature type. My $response ...

2

Ensembl Genomes REST API - GET genetree/id/:id

http://rest.ensemblgenomes.org/documentation/info/genetree

About the Ensembl Genomes Project. Retrieves a gene tree dump for a gene tree stable identifier. An Ensembl genetree ID. Return the aligned string if true. Otherwise, return the original sequence (no insertions). Name of the callback subroutine to be returned by the requested JSONP response. Required ONLY when using JSONP as the serialisation method. Please see the user guide. Return the aligned sequence encoded in CIGAR format. The format of a NH (New Hampshire) request. Prune the tree by taxon. N unles...

3

Ensembl Genomes REST API - GET info/comparas

http://rest.ensemblgenomes.org/documentation/info/comparas

About the Ensembl Genomes Project. Lists all available comparative genomics databases and their data release. Name of the callback subroutine to be returned by the requested JSONP response. Required ONLY when using JSONP as the serialisation method. Please see the user guide. Use strict; use warnings; use HTTP: Tiny; my $http = HTTP: Tiny- new(); my $server = 'http:/ rest.ensemblgenomes.org'; my $ext = '/info/comparas? Url = URI.parse(server) http = Net: HTTP.new(url.host, url.port) reque...200 puts Inva...

4

Ensembl Genomes REST API - GET info/compara/methods

http://rest.ensemblgenomes.org/documentation/info/compara_methods

About the Ensembl Genomes Project. List all compara analyses available (an analysis defines the type of comparative data). Name of the callback subroutine to be returned by the requested JSONP response. Required ONLY when using JSONP as the serialisation method. Please see the user guide. The class of the method to query for. Regular expression patterns are supported. Name of the compara database to use. Multiple comparas may exist on a server when accessing Ensembl Genomes data. R = requests.get(ser...

5

Ensembl Genomes REST API - GET xrefs/name/:species/:name

http://rest.ensemblgenomes.org/documentation/info/xref_name

About the Ensembl Genomes Project. Performs a lookup based upon the primary accession or display label of an external reference and returning the information we hold about the entry. Symbol or display name of a gene. Name of the callback subroutine to be returned by the requested JSONP response. Required ONLY when using JSONP as the serialisation method. Please see the user guide. Restrict the search to a database other than the default. Useful if you need to use a DB other than core. R = requests.ge...

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LINKS TO THIS WEBSITE

fungi.ensembl.org fungi.ensembl.org

Ensembl Fungi

http://fungi.ensembl.org/info/website/help/index.html

Search for a gene. Search for a genome. Eg type sac to find Saccharomyces. For easy access to commonly used genomes, drag from the bottom list to the top one · Save. Aspergillus nidulans FGSC A4. Puccinia graminis f. sp. tritici CRL 75-36-700-3. Acidomyces richmondensis BFW (. Acremonium chrysogenum ATCC 11550 (. Acremonium chrysogenum ATCC 11550. Agaricus bisporus var. bisporus H97 (. Agaricus bisporus var. bisporus H97. Agaricus bisporus var. burnettii JB137-S8 (. Allomyces macrogynus ATCC 38327 (.

protists.ensembl.org protists.ensembl.org

Ensembl Protists

http://protists.ensembl.org/info/website/help/index.html

Search for a gene. Search for a genome. Eg type pla to find Plasmodium. For easy access to commonly used genomes, drag from the bottom list to the top one · Save. Leishmania major strain Friedlin. Acanthamoeba castellanii str. Neff (. Acanthamoeba castellanii str. Neff. Babesia microti strain RI (. Babesia microti strain RI. Bigelowiella natans (GCA 000002455) (. Bigelowiella natans (GCA 000002455). Capsaspora owczarzaki ATCC 30864 (. Capsaspora owczarzaki ATCC 30864. Chroomonas mesostigmatica CCMP1168 (.

github.com github.com

Home · EnsemblGenomes/eg-rest Wiki · GitHub

https://github.com/EnsemblGenomes/eg-rest/wiki

Dan Bolser edited this page. Mar 8, 2016. Middot; 5 revisions. Clone this wiki locally. Provides a fully featured REST server. Based on the codebase. Provided by our sister project Ensembl. Since Ensembl Genomes has different content and use-cases to Ensembl, particularly when dealing with over 15,000 bacterial genomes, the Ensembl Genomes REST server provides some additional endpoints, which are available as plugins in this repository and described below. Find information about a given genome. To suppor...

bacteria.ensembl.org bacteria.ensembl.org

Ensembl Bacteria

http://bacteria.ensembl.org/info/about/species.html

Search for a gene. Search for a genome. Eg type esc to find Escherichia. Access to over 40,000. Search for a gene. Type the name of a gene or other identifier into the search box above. Click in the 'browse a genome' box above and start typing your genome name to find matching genomes. View full list of all Ensembl Bacteria species. Access Ensembl Bacteria programmatically. What's New in Release 32. To access Ensembl Genomes data from any programming language, try our REST service. New genomes, 15. Throu...

bacteria.ensembl.org bacteria.ensembl.org

Ensembl Bacteria

http://bacteria.ensembl.org/info/website/help/index.html

Search for a gene. Search for a genome. Eg type esc to find Escherichia. Access to over 40,000. Search for a gene. Type the name of a gene or other identifier into the search box above. Click in the 'browse a genome' box above and start typing your genome name to find matching genomes. View full list of all Ensembl Bacteria species. Access Ensembl Bacteria programmatically. What's New in Release 32. To access Ensembl Genomes data from any programming language, try our REST service. New genomes, 15. Throu...

bacteria.ensembl.org bacteria.ensembl.org

Ensembl Bacteria

http://bacteria.ensembl.org/UserData/ManageData?time=1432113509

Search for a gene. Search for a genome. Eg type esc to find Escherichia. Access to over 40,000. Search for a gene. Type the name of a gene or other identifier into the search box above. Click in the 'browse a genome' box above and start typing your genome name to find matching genomes. View full list of all Ensembl Bacteria species. Access Ensembl Bacteria programmatically. What's New in Release 32. To access Ensembl Genomes data from any programming language, try our REST service. New genomes, 15. Throu...

dev.gramene.org dev.gramene.org

Gramene

http://dev.gramene.org/tools.html

We provide a number of ready-made tools for processing your data. At the moment, small datasets can be uploaded to our servers and processed online; for larger datasets, we provide an API script that can be downloaded (you will also need to install our Perl API. In the near future we aim to offer an intermediate service, whereby medium-to-large data sets can be submitted to a queue, similar to BLAST. Quickly search our genomes for your protein sequence. Search our genomes for your DNA or protein sequence.

ensembl.gramene.org ensembl.gramene.org

Gramene

http://ensembl.gramene.org/tools.html

We provide a number of ready-made tools for processing both our data and yours. We routinely delete results from our servers after 10 days, but if you have an ensembl account. You will be able to save the results indefinitely. Analyse your own variants and predict the functional consequences of known and unknown variants via our Variant Effect Predictor (VEP) tool. Quickly search our genomes for your protein sequence. Search our genomes for your DNA or protein sequence. Ensembl Genomes REST server.

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Ensembl Rest API - Ensembl REST API Endpoints

About the Ensembl Project. Ensembl REST API Endpoints. Uses the given identifier to return the archived sequence. Retrieve the archived sequence for a set of identifiers. Retrieves a gene tree dump for a gene tree stable identifier. Retrieves a gene tree that contains the stable identifier. Retrieves a gene tree containing the gene identified by a symbol. Retrieves genomic alignments as separate blocks based on a region and species. Retrieves homology information (orthologs) by Ensembl gene id. List the ...

rest.ensemblgenomes.org rest.ensemblgenomes.org

Ensembl Rest API - Ensembl Genomes REST API Endpoints

About the Ensembl Project. Ensembl Genomes REST API Endpoints. Uses the given identifier to return the archived sequence. Retrieve the archived sequence for a set of identifiers. Retrieves gene family information by ID. Retrieves gene families to which a gene belongs. Retrieves gene families to which a gene belongs. Retrieves a gene tree dump for a gene tree stable identifier. Retrieves a gene tree that contains the stable identifier. Retrieves a gene tree containing the gene identified by a symbol.

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