Ensembl Rest API - GET sequence/id/:id

Request multiple types of sequence by stable identifier. Supports feature masking and expand options.

Parameters

Required

Name	Type	Description	Default	Example Values
id	`String`	An Ensembl stable ID	`-`	`ENSG00000157764` `ENSG00000157764.fasta (supported on some deployments)`

Optional

Name	Type	Description	Default	Example Values
callback	`String`	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.	`-`	`randomlygeneratedname`
db_type	`String`	Restrict the search to a database other than the default. Useful if you need to use a DB other than core	`-`	`core`
end	`Int`	Trim the end of the sequence by this many basepairs. Trimming is relative to reading direction and in the coordinate system of the stable identifier. Parameter can not be used in conjunction with expand_5prime or expand_3prime.	`-`	`1000`
expand_3prime	`Int`	Expand the sequence downstream of the sequence by this many basepairs. Only available when using genomic sequence type.	`-`	`1000`
expand_5prime	`Int`	Expand the sequence upstream of the sequence by this many basepairs. Only available when using genomic sequence type.	`-`	`1000`
format	`Enum(fasta)`	Format of the data	`-`	`fasta`
mask	`Enum(hard,soft)`	Request the sequence masked for repeat sequences. Hard will mask all repeats as N's and soft will mask repeats as lowercased characters. Only available when using genomic sequence type.	`-`	`hard`
mask_feature	`Boolean`	Mask features on the sequence. If sequence is genomic, mask introns. If sequence is cDNA, mask UTRs. Incompatible with the 'mask' option	`0`	`-`
multiple_sequences	`Boolean`	Allow the service to return more than 1 sequence per identifier. This is useful when querying for a gene but using a type such as protein.	`0`	`-`
object_type	`String`	Filter by feature type	`-`	`gene`
species	`String`	Species name/alias	`-`	`homo_sapiens`
start	`Int`	Trim the start of the sequence by this many basepairs. Trimming is relative to reading direction and in the coordinate system of the stable identifier. Parameter can not be used in conjunction with expand_5prime or expand_3prime.	`-`	`1000`
type	`Enum(genomic,cds,cdna,protein)`	Type of sequence. Defaults to genomic where applicable, i.e. not translations. cdna refers to the spliced transcript sequence with UTR; cds refers to the spliced transcript sequence without UTR.	`genomic`	`cds`

Example Requests

/sequence/id/ENSG00000157764?content-type=text/plain

use strict;
use warnings;
 
use HTTP::Tiny;
 
my $http = HTTP::Tiny->new();
 
my $server = 'http://rest.ensembl.org';
my $ext = '/sequence/id/ENSG00000157764?';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'text/plain' }
});
 
die "Failed!\n" unless $response->{success};
 
 
print "$response->{content}\n";

import requests, sys
 
server = "http://rest.ensembl.org"
ext = "/sequence/id/ENSG00000157764?"
 
r = requests.get(server+ext, headers={ "Content-Type" : "text/plain"})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
 
print r.text

import requests, sys
 
server = "http://rest.ensembl.org"
ext = "/sequence/id/ENSG00000157764?"
 
r = requests.get(server+ext, headers={ "Content-Type" : "text/plain"})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
 
print(r.text)

require 'net/http'
require 'uri'
 
server='http://rest.ensembl.org'
path = '/sequence/id/ENSG00000157764?'
 
url = URI.parse(server)
http = Net::HTTP.new(url.host, url.port)
 
request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/plain'})
 
response = http.request(request)
 
if response.code != "200"
  puts "Invalid response: #{response.code}"
  puts response.body
  exit
end
 
 
puts response.body

import java.net.URL;
import java.net.URLConnection;
import java.net.HttpURLConnection;
import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.IOException;
import java.io.Reader;
 
 
public class EnsemblRest {
 
  public static void main(String[] args) throws Exception {
    String server = "http://rest.ensembl.org";
    String ext = "/sequence/id/ENSG00000157764?";
    URL url = new URL(server + ext);
 
    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    httpConnection.setRequestProperty("Content-Type", "text/plain");
    
 
    InputStream response = connection.getInputStream();
    int responseCode = httpConnection.getResponseCode();
 
    if(responseCode != 200) {
      throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
    }
 
    String output;
    Reader reader = null;
    try {
      reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
      StringBuilder builder = new StringBuilder();
      char[] buffer = new char[8192];
      int read;
      while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
        builder.append(buffer, 0, read);
      }
      output = builder.toString();
    } 
    finally {
        if (reader != null) try {
          reader.close(); 
        } catch (IOException logOrIgnore) {
          logOrIgnore.printStackTrace();
        }
    }
 
    System.out.println(output);
  }
}

library(httr)
library(jsonlite)
library(xml2)
 
server <- "http://rest.ensembl.org"
ext <- "/sequence/id/ENSG00000157764?"
 
r <- GET(paste(server, ext, sep = ""), content_type("text/plain"))
 
stop_for_status(r)
 
 
print(content(r))

 
curl 'http://rest.ensembl.org/sequence/id/ENSG00000157764?' -H 'Content-type:text/plain'

wget -q --header='Content-type:text/plain' 'http://rest.ensembl.org/sequence/id/ENSG00000157764?'  -O -

/sequence/id/CCDS5863.1?content-type=text/x-fasta;object_type=transcript;db_type=otherfeatures;type=cds;species=human

 >CCDS5863.1.1
ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC
GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC
CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT
ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG
GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG
GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT
ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT
CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC
CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT
CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT
CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA
GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA
ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC
TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT
GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA
CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA
CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT
CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA
GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT
GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT
ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA
GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA
CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA
CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG
GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT
GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC
ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT
CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT
GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT
AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG
AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG
GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT
GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC
AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG
GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA
AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA
TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA
GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT
GGTGCGTTTCCTGTCCACTGA

use strict;
use warnings;
 
use HTTP::Tiny;
 
my $http = HTTP::Tiny->new();
 
my $server = 'http://rest.ensembl.org';
my $ext = '/sequence/id/CCDS5863.1?object_type=transcript;db_type=otherfeatures;type=cds;species=human';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'text/x-fasta' }
});
 
die "Failed!\n" unless $response->{success};
 
 
print "$response->{content}\n";

import requests, sys
 
server = "http://rest.ensembl.org"
ext = "/sequence/id/CCDS5863.1?object_type=transcript;db_type=otherfeatures;type=cds;species=human"
 
r = requests.get(server+ext, headers={ "Content-Type" : "text/x-fasta"})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
 
print r.text

import requests, sys
 
server = "http://rest.ensembl.org"
ext = "/sequence/id/CCDS5863.1?object_type=transcript;db_type=otherfeatures;type=cds;species=human"
 
r = requests.get(server+ext, headers={ "Content-Type" : "text/x-fasta"})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
 
print(r.text)

require 'net/http'
require 'uri'
 
server='http://rest.ensembl.org'
path = '/sequence/id/CCDS5863.1?object_type=transcript;db_type=otherfeatures;type=cds;species=human'
 
url = URI.parse(server)
http = Net::HTTP.new(url.host, url.port)
 
request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/x-fasta'})
 
response = http.request(request)
 
if response.code != "200"
  puts "Invalid response: #{response.code}"
  puts response.body
  exit
end
 
 
puts response.body

import java.net.URL;
import java.net.URLConnection;
import java.net.HttpURLConnection;
import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.IOException;
import java.io.Reader;
 
 
public class EnsemblRest {
 
  public static void main(String[] args) throws Exception {
    String server = "http://rest.ensembl.org";
    String ext = "/sequence/id/CCDS5863.1?object_type=transcript;db_type=otherfeatures;type=cds;species=human";
    URL url = new URL(server + ext);
 
    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    httpConnection.setRequestProperty("Content-Type", "text/x-fasta");
    
 
    InputStream response = connection.getInputStream();
    int responseCode = httpConnection.getResponseCode();
 
    if(responseCode != 200) {
      throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
    }
 
    String output;
    Reader reader = null;
    try {
      reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
      StringBuilder builder = new StringBuilder();
      char[] buffer = new char[8192];
      int read;
      while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
        builder.append(buffer, 0, read);
      }
      output = builder.toString();
    } 
    finally {
        if (reader != null) try {
          reader.close(); 
        } catch (IOException logOrIgnore) {
          logOrIgnore.printStackTrace();
        }
    }
 
    System.out.println(output);
  }
}

library(httr)
library(jsonlite)
library(xml2)
 
server <- "http://rest.ensembl.org"
ext <- "/sequence/id/CCDS5863.1?object_type=transcript;db_type=otherfeatures;type=cds;species=human"
 
r <- GET(paste(server, ext, sep = ""), content_type("text/x-fasta"))
 
stop_for_status(r)
 
 
print(content(r))

 
curl 'http://rest.ensembl.org/sequence/id/CCDS5863.1?object_type=transcript;db_type=otherfeatures;type=cds;species=human' -H 'Content-type:text/x-fasta'

wget -q --header='Content-type:text/x-fasta' 'http://rest.ensembl.org/sequence/id/CCDS5863.1?object_type=transcript;db_type=otherfeatures;type=cds;species=human'  -O -

/sequence/id/ENST00000288602?type=cdna;content-type=text/x-fasta

use strict;
use warnings;
 
use HTTP::Tiny;
 
my $http = HTTP::Tiny->new();
 
my $server = 'http://rest.ensembl.org';
my $ext = '/sequence/id/ENST00000288602?type=cdna';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'text/x-fasta' }
});
 
die "Failed!\n" unless $response->{success};
 
 
print "$response->{content}\n";

import requests, sys
 
server = "http://rest.ensembl.org"
ext = "/sequence/id/ENST00000288602?type=cdna"
 
r = requests.get(server+ext, headers={ "Content-Type" : "text/x-fasta"})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
 
print r.text

import requests, sys
 
server = "http://rest.ensembl.org"
ext = "/sequence/id/ENST00000288602?type=cdna"
 
r = requests.get(server+ext, headers={ "Content-Type" : "text/x-fasta"})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
 
print(r.text)

require 'net/http'
require 'uri'
 
server='http://rest.ensembl.org'
path = '/sequence/id/ENST00000288602?type=cdna'
 
url = URI.parse(server)
http = Net::HTTP.new(url.host, url.port)
 
request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/x-fasta'})
 
response = http.request(request)
 
if response.code != "200"
  puts "Invalid response: #{response.code}"
  puts response.body
  exit
end
 
 
puts response.body

import java.net.URL;
import java.net.URLConnection;
import java.net.HttpURLConnection;
import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.IOException;
import java.io.Reader;
 
 
public class EnsemblRest {
 
  public static void main(String[] args) throws Exception {
    String server = "http://rest.ensembl.org";
    String ext = "/sequence/id/ENST00000288602?type=cdna";
    URL url = new URL(server + ext);
 
    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    httpConnection.setRequestProperty("Content-Type", "text/x-fasta");
    
 
    InputStream response = connection.getInputStream();
    int responseCode = httpConnection.getResponseCode();
 
    if(responseCode != 200) {
      throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
    }
 
    String output;
    Reader reader = null;
    try {
      reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
      StringBuilder builder = new StringBuilder();
      char[] buffer = new char[8192];
      int read;
      while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
        builder.append(buffer, 0, read);
      }
      output = builder.toString();
    } 
    finally {
        if (reader != null) try {
          reader.close(); 
        } catch (IOException logOrIgnore) {
          logOrIgnore.printStackTrace();
        }
    }
 
    System.out.println(output);
  }
}

library(httr)
library(jsonlite)
library(xml2)
 
server <- "http://rest.ensembl.org"
ext <- "/sequence/id/ENST00000288602?type=cdna"
 
r <- GET(paste(server, ext, sep = ""), content_type("text/x-fasta"))
 
stop_for_status(r)
 
 
print(content(r))

 
curl 'http://rest.ensembl.org/sequence/id/ENST00000288602?type=cdna' -H 'Content-type:text/x-fasta'

wget -q --header='Content-type:text/x-fasta' 'http://rest.ensembl.org/sequence/id/ENST00000288602?type=cdna'  -O -

/sequence/id/ENST00000288602?content-type=text/x-fasta;type=cds

 >ENST00000288602.11
ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC
GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC
CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT
ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG
GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG
GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT
ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT
CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC
CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT
CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT
CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA
GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA
ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC
TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT
GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA
CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA
CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT
CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA
GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT
GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGCCCCTTTGAACCAGCTGATGCGC
TGTCTTCGGAAATACCAATCCCGGACTCCCAGTCCCCTCCTACATTCTGTCCCCAGTGAA
ATAGTGTTTGATTTTGAGCCTGGCCCAGTGTTCAGAGGATCAACCACAGGTTTGTCTGCT
ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA
GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA
CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA
CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG
GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT
GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC
ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT
CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT
GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT
AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG
AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG
GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT
GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC
AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG
GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA
AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA
TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA
GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT
GGTGCGTTTCCTGTCCACTGA

use strict;
use warnings;
 
use HTTP::Tiny;
 
my $http = HTTP::Tiny->new();
 
my $server = 'http://rest.ensembl.org';
my $ext = '/sequence/id/ENST00000288602?type=cds';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'text/x-fasta' }
});
 
die "Failed!\n" unless $response->{success};
 
 
print "$response->{content}\n";

import requests, sys
 
server = "http://rest.ensembl.org"
ext = "/sequence/id/ENST00000288602?type=cds"
 
r = requests.get(server+ext, headers={ "Content-Type" : "text/x-fasta"})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
 
print r.text

import requests, sys
 
server = "http://rest.ensembl.org"
ext = "/sequence/id/ENST00000288602?type=cds"
 
r = requests.get(server+ext, headers={ "Content-Type" : "text/x-fasta"})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
 
print(r.text)

require 'net/http'
require 'uri'
 
server='http://rest.ensembl.org'
path = '/sequence/id/ENST00000288602?type=cds'
 
url = URI.parse(server)
http = Net::HTTP.new(url.host, url.port)
 
request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/x-fasta'})
 
response = http.request(request)
 
if response.code != "200"
  puts "Invalid response: #{response.code}"
  puts response.body
  exit
end
 
 
puts response.body

import java.net.URL;
import java.net.URLConnection;
import java.net.HttpURLConnection;
import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.IOException;
import java.io.Reader;
 
 
public class EnsemblRest {
 
  public static void main(String[] args) throws Exception {
    String server = "http://rest.ensembl.org";
    String ext = "/sequence/id/ENST00000288602?type=cds";
    URL url = new URL(server + ext);
 
    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    httpConnection.setRequestProperty("Content-Type", "text/x-fasta");
    
 
    InputStream response = connection.getInputStream();
    int responseCode = httpConnection.getResponseCode();
 
    if(responseCode != 200) {
      throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
    }
 
    String output;
    Reader reader = null;
    try {
      reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
      StringBuilder builder = new StringBuilder();
      char[] buffer = new char[8192];
      int read;
      while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
        builder.append(buffer, 0, read);
      }
      output = builder.toString();
    } 
    finally {
        if (reader != null) try {
          reader.close(); 
        } catch (IOException logOrIgnore) {
          logOrIgnore.printStackTrace();
        }
    }
 
    System.out.println(output);
  }
}

library(httr)
library(jsonlite)
library(xml2)
 
server <- "http://rest.ensembl.org"
ext <- "/sequence/id/ENST00000288602?type=cds"
 
r <- GET(paste(server, ext, sep = ""), content_type("text/x-fasta"))
 
stop_for_status(r)
 
 
print(content(r))

 
curl 'http://rest.ensembl.org/sequence/id/ENST00000288602?type=cds' -H 'Content-type:text/x-fasta'

wget -q --header='Content-type:text/x-fasta' 'http://rest.ensembl.org/sequence/id/ENST00000288602?type=cds'  -O -

/sequence/id/ENSE00001154485?content-type=text/x-fasta;type=genomic

 >ENSE00001154485.4 chromosome:GRCh38:7:140924566:140924742:-1
CCGACAGCGGCCGCTCGGGCCCCGGCTCTCGGTTATAAGATGGCGGCGCTGAGCGGTGGC
GGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAACGGGGACATGGAGCCCGAGGCC
GGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGACCCTGCCATTCCGGAGGAG

use strict;
use warnings;
 
use HTTP::Tiny;
 
my $http = HTTP::Tiny->new();
 
my $server = 'http://rest.ensembl.org';
my $ext = '/sequence/id/ENSE00001154485?type=genomic';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'text/x-fasta' }
});
 
die "Failed!\n" unless $response->{success};
 
 
print "$response->{content}\n";

import requests, sys
 
server = "http://rest.ensembl.org"
ext = "/sequence/id/ENSE00001154485?type=genomic"
 
r = requests.get(server+ext, headers={ "Content-Type" : "text/x-fasta"})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
 
print r.text

import requests, sys
 
server = "http://rest.ensembl.org"
ext = "/sequence/id/ENSE00001154485?type=genomic"
 
r = requests.get(server+ext, headers={ "Content-Type" : "text/x-fasta"})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
 
print(r.text)

require 'net/http'
require 'uri'
 
server='http://rest.ensembl.org'
path = '/sequence/id/ENSE00001154485?type=genomic'
 
url = URI.parse(server)
http = Net::HTTP.new(url.host, url.port)
 
request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/x-fasta'})
 
response = http.request(request)
 
if response.code != "200"
  puts "Invalid response: #{response.code}"
  puts response.body
  exit
end
 
 
puts response.body

import java.net.URL;
import java.net.URLConnection;
import java.net.HttpURLConnection;
import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.IOException;
import java.io.Reader;
 
 
public class EnsemblRest {
 
  public static void main(String[] args) throws Exception {
    String server = "http://rest.ensembl.org";
    String ext = "/sequence/id/ENSE00001154485?type=genomic";
    URL url = new URL(server + ext);
 
    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    httpConnection.setRequestProperty("Content-Type", "text/x-fasta");
    
 
    InputStream response = connection.getInputStream();
    int responseCode = httpConnection.getResponseCode();
 
    if(responseCode != 200) {
      throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
    }
 
    String output;
    Reader reader = null;
    try {
      reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
      StringBuilder builder = new StringBuilder();
      char[] buffer = new char[8192];
      int read;
      while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
        builder.append(buffer, 0, read);
      }
      output = builder.toString();
    } 
    finally {
        if (reader != null) try {
          reader.close(); 
        } catch (IOException logOrIgnore) {
          logOrIgnore.printStackTrace();
        }
    }
 
    System.out.println(output);
  }
}

library(httr)
library(jsonlite)
library(xml2)
 
server <- "http://rest.ensembl.org"
ext <- "/sequence/id/ENSE00001154485?type=genomic"
 
r <- GET(paste(server, ext, sep = ""), content_type("text/x-fasta"))
 
stop_for_status(r)
 
 
print(content(r))

 
curl 'http://rest.ensembl.org/sequence/id/ENSE00001154485?type=genomic' -H 'Content-type:text/x-fasta'

wget -q --header='Content-type:text/x-fasta' 'http://rest.ensembl.org/sequence/id/ENSE00001154485?type=genomic'  -O -

/sequence/id/ENSE00001154485?type=genomic;content-type=text/x-fasta;expand_5prime=10

use strict;
use warnings;
 
use HTTP::Tiny;
 
my $http = HTTP::Tiny->new();
 
my $server = 'http://rest.ensembl.org';
my $ext = '/sequence/id/ENSE00001154485?expand_5prime=10;type=genomic';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'text/x-fasta' }
});
 
die "Failed!\n" unless $response->{success};
 
 
print "$response->{content}\n";

import requests, sys
 
server = "http://rest.ensembl.org"
ext = "/sequence/id/ENSE00001154485?expand_5prime=10;type=genomic"
 
r = requests.get(server+ext, headers={ "Content-Type" : "text/x-fasta"})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
 
print r.text

import requests, sys
 
server = "http://rest.ensembl.org"
ext = "/sequence/id/ENSE00001154485?expand_5prime=10;type=genomic"
 
r = requests.get(server+ext, headers={ "Content-Type" : "text/x-fasta"})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
 
print(r.text)

require 'net/http'
require 'uri'
 
server='http://rest.ensembl.org'
path = '/sequence/id/ENSE00001154485?expand_5prime=10;type=genomic'
 
url = URI.parse(server)
http = Net::HTTP.new(url.host, url.port)
 
request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/x-fasta'})
 
response = http.request(request)
 
if response.code != "200"
  puts "Invalid response: #{response.code}"
  puts response.body
  exit
end
 
 
puts response.body

import java.net.URL;
import java.net.URLConnection;
import java.net.HttpURLConnection;
import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.IOException;
import java.io.Reader;
 
 
public class EnsemblRest {
 
  public static void main(String[] args) throws Exception {
    String server = "http://rest.ensembl.org";
    String ext = "/sequence/id/ENSE00001154485?expand_5prime=10;type=genomic";
    URL url = new URL(server + ext);
 
    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    httpConnection.setRequestProperty("Content-Type", "text/x-fasta");
    
 
    InputStream response = connection.getInputStream();
    int responseCode = httpConnection.getResponseCode();
 
    if(responseCode != 200) {
      throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
    }
 
    String output;
    Reader reader = null;
    try {
      reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
      StringBuilder builder = new StringBuilder();
      char[] buffer = new char[8192];
      int read;
      while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
        builder.append(buffer, 0, read);
      }
      output = builder.toString();
    } 
    finally {
        if (reader != null) try {
          reader.close(); 
        } catch (IOException logOrIgnore) {
          logOrIgnore.printStackTrace();
        }
    }
 
    System.out.println(output);
  }
}

library(httr)
library(jsonlite)
library(xml2)
 
server <- "http://rest.ensembl.org"
ext <- "/sequence/id/ENSE00001154485?expand_5prime=10;type=genomic"
 
r <- GET(paste(server, ext, sep = ""), content_type("text/x-fasta"))
 
stop_for_status(r)
 
 
print(content(r))

 
curl 'http://rest.ensembl.org/sequence/id/ENSE00001154485?expand_5prime=10;type=genomic' -H 'Content-type:text/x-fasta'

wget -q --header='Content-type:text/x-fasta' 'http://rest.ensembl.org/sequence/id/ENSE00001154485?expand_5prime=10;type=genomic'  -O -

/sequence/id/ENSG00000157764?content-type=text/x-seqxml%2Bxml;multiple_sequences=1;type=protein

use strict;
use warnings;
 
use HTTP::Tiny;
 
my $http = HTTP::Tiny->new();
 
my $server = 'http://rest.ensembl.org';
my $ext = '/sequence/id/ENSG00000157764?multiple_sequences=1;type=protein';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'text/x-seqxml+xml' }
});
 
die "Failed!\n" unless $response->{success};
 
 
print "$response->{content}\n";

import requests, sys
 
server = "http://rest.ensembl.org"
ext = "/sequence/id/ENSG00000157764?multiple_sequences=1;type=protein"
 
r = requests.get(server+ext, headers={ "Content-Type" : "text/x-seqxml+xml"})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
 
print r.text

import requests, sys
 
server = "http://rest.ensembl.org"
ext = "/sequence/id/ENSG00000157764?multiple_sequences=1;type=protein"
 
r = requests.get(server+ext, headers={ "Content-Type" : "text/x-seqxml+xml"})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
 
print(r.text)

require 'net/http'
require 'uri'
 
server='http://rest.ensembl.org'
path = '/sequence/id/ENSG00000157764?multiple_sequences=1;type=protein'
 
url = URI.parse(server)
http = Net::HTTP.new(url.host, url.port)
 
request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/x-seqxml+xml'})
 
response = http.request(request)
 
if response.code != "200"
  puts "Invalid response: #{response.code}"
  puts response.body
  exit
end
 
 
puts response.body

import java.net.URL;
import java.net.URLConnection;
import java.net.HttpURLConnection;
import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.IOException;
import java.io.Reader;
 
 
public class EnsemblRest {
 
  public static void main(String[] args) throws Exception {
    String server = "http://rest.ensembl.org";
    String ext = "/sequence/id/ENSG00000157764?multiple_sequences=1;type=protein";
    URL url = new URL(server + ext);
 
    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    httpConnection.setRequestProperty("Content-Type", "text/x-seqxml+xml");
    
 
    InputStream response = connection.getInputStream();
    int responseCode = httpConnection.getResponseCode();
 
    if(responseCode != 200) {
      throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
    }
 
    String output;
    Reader reader = null;
    try {
      reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
      StringBuilder builder = new StringBuilder();
      char[] buffer = new char[8192];
      int read;
      while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
        builder.append(buffer, 0, read);
      }
      output = builder.toString();
    } 
    finally {
        if (reader != null) try {
          reader.close(); 
        } catch (IOException logOrIgnore) {
          logOrIgnore.printStackTrace();
        }
    }
 
    System.out.println(output);
  }
}

library(httr)
library(jsonlite)
library(xml2)
 
server <- "http://rest.ensembl.org"
ext <- "/sequence/id/ENSG00000157764?multiple_sequences=1;type=protein"
 
r <- GET(paste(server, ext, sep = ""), content_type("text/x-seqxml+xml"))
 
stop_for_status(r)
 
 
print(content(r))

 
curl 'http://rest.ensembl.org/sequence/id/ENSG00000157764?multiple_sequences=1;type=protein' -H 'Content-type:text/x-seqxml+xml'

wget -q --header='Content-type:text/x-seqxml+xml' 'http://rest.ensembl.org/sequence/id/ENSG00000157764?multiple_sequences=1;type=protein'  -O -

/sequence/id/GENSCAN00000000001?content-type=application/json;object_type=predictiontranscript;type=protein;db_type=core;species=homo_sapiens

use strict;
use warnings;
 
use HTTP::Tiny;
 
my $http = HTTP::Tiny->new();
 
my $server = 'http://rest.ensembl.org';
my $ext = '/sequence/id/GENSCAN00000000001?type=protein;db_type=core;species=homo_sapiens;object_type=predictiontranscript';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'application/json' }
});
 
die "Failed!\n" unless $response->{success};
 
 
use JSON;
use Data::Dumper;
if(length $response->{content}) {
  my $hash = decode_json($response->{content});
  local $Data::Dumper::Terse = 1;
  local $Data::Dumper::Indent = 1;
  print Dumper $hash;
  print "\n";
}

import requests, sys
 
server = "http://rest.ensembl.org"
ext = "/sequence/id/GENSCAN00000000001?type=protein;db_type=core;species=homo_sapiens;object_type=predictiontranscript"
 
r = requests.get(server+ext, headers={ "Content-Type" : "application/json"})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
decoded = r.json()
print repr(decoded)

import requests, sys
 
server = "http://rest.ensembl.org"
ext = "/sequence/id/GENSCAN00000000001?type=protein;db_type=core;species=homo_sapiens;object_type=predictiontranscript"
 
r = requests.get(server+ext, headers={ "Content-Type" : "application/json"})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
decoded = r.json()
print(repr(decoded))

require 'net/http'
require 'uri'
 
server='http://rest.ensembl.org'
path = '/sequence/id/GENSCAN00000000001?type=protein;db_type=core;species=homo_sapiens;object_type=predictiontranscript'
 
url = URI.parse(server)
http = Net::HTTP.new(url.host, url.port)
 
request = Net::HTTP::Get.new(path, {'Content-Type' => 'application/json'})
 
response = http.request(request)
 
if response.code != "200"
  puts "Invalid response: #{response.code}"
  puts response.body
  exit
end
 
 
require 'rubygems'
require 'json'
require 'yaml'
 
result = JSON.parse(response.body)
puts YAML::dump(result)

import java.net.URL;
import java.net.URLConnection;
import java.net.HttpURLConnection;
import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.IOException;
import java.io.Reader;
 
 
public class EnsemblRest {
 
  public static void main(String[] args) throws Exception {
    String server = "http://rest.ensembl.org";
    String ext = "/sequence/id/GENSCAN00000000001?type=protein;db_type=core;species=homo_sapiens;object_type=predictiontranscript";
    URL url = new URL(server + ext);
 
    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    httpConnection.setRequestProperty("Content-Type", "application/json");
    
 
    InputStream response = connection.getInputStream();
    int responseCode = httpConnection.getResponseCode();
 
    if(responseCode != 200) {
      throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
    }
 
    String output;
    Reader reader = null;
    try {
      reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
      StringBuilder builder = new StringBuilder();
      char[] buffer = new char[8192];
      int read;
      while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
        builder.append(buffer, 0, read);
      }
      output = builder.toString();
    } 
    finally {
        if (reader != null) try {
          reader.close(); 
        } catch (IOException logOrIgnore) {
          logOrIgnore.printStackTrace();
        }
    }
 
    System.out.println(output);
  }
}

library(httr)
library(jsonlite)
library(xml2)
 
server <- "http://rest.ensembl.org"
ext <- "/sequence/id/GENSCAN00000000001?type=protein;db_type=core;species=homo_sapiens;object_type=predictiontranscript"
 
r <- GET(paste(server, ext, sep = ""), content_type("application/json"))
 
stop_for_status(r)
 
# use this if you get a simple nested list back, otherwise inspect its structure
# head(data.frame(t(sapply(content(r),c))))
head(fromJSON(toJSON(content(r))))

 
curl 'http://rest.ensembl.org/sequence/id/GENSCAN00000000001?type=protein;db_type=core;species=homo_sapiens;object_type=predictiontranscript' -H 'Content-type:application/json'

wget -q --header='Content-type:application/json' 'http://rest.ensembl.org/sequence/id/GENSCAN00000000001?type=protein;db_type=core;species=homo_sapiens;object_type=predictiontranscript'  -O -

/sequence/id/ENSP00000288602?content-type=application/json

use strict;
use warnings;
 
use HTTP::Tiny;
 
my $http = HTTP::Tiny->new();
 
my $server = 'http://rest.ensembl.org';
my $ext = '/sequence/id/ENSP00000288602?';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'application/json' }
});
 
die "Failed!\n" unless $response->{success};
 
 
use JSON;
use Data::Dumper;
if(length $response->{content}) {
  my $hash = decode_json($response->{content});
  local $Data::Dumper::Terse = 1;
  local $Data::Dumper::Indent = 1;
  print Dumper $hash;
  print "\n";
}

import requests, sys
 
server = "http://rest.ensembl.org"
ext = "/sequence/id/ENSP00000288602?"
 
r = requests.get(server+ext, headers={ "Content-Type" : "application/json"})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
decoded = r.json()
print repr(decoded)

import requests, sys
 
server = "http://rest.ensembl.org"
ext = "/sequence/id/ENSP00000288602?"
 
r = requests.get(server+ext, headers={ "Content-Type" : "application/json"})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
decoded = r.json()
print(repr(decoded))

require 'net/http'
require 'uri'
 
server='http://rest.ensembl.org'
path = '/sequence/id/ENSP00000288602?'
 
url = URI.parse(server)
http = Net::HTTP.new(url.host, url.port)
 
request = Net::HTTP::Get.new(path, {'Content-Type' => 'application/json'})
 
response = http.request(request)
 
if response.code != "200"
  puts "Invalid response: #{response.code}"
  puts response.body
  exit
end
 
 
require 'rubygems'
require 'json'
require 'yaml'
 
result = JSON.parse(response.body)
puts YAML::dump(result)

import java.net.URL;
import java.net.URLConnection;
import java.net.HttpURLConnection;
import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.IOException;
import java.io.Reader;
 
 
public class EnsemblRest {
 
  public static void main(String[] args) throws Exception {
    String server = "http://rest.ensembl.org";
    String ext = "/sequence/id/ENSP00000288602?";
    URL url = new URL(server + ext);
 
    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    httpConnection.setRequestProperty("Content-Type", "application/json");
    
 
    InputStream response = connection.getInputStream();
    int responseCode = httpConnection.getResponseCode();
 
    if(responseCode != 200) {
      throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
    }
 
    String output;
    Reader reader = null;
    try {
      reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
      StringBuilder builder = new StringBuilder();
      char[] buffer = new char[8192];
      int read;
      while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
        builder.append(buffer, 0, read);
      }
      output = builder.toString();
    } 
    finally {
        if (reader != null) try {
          reader.close(); 
        } catch (IOException logOrIgnore) {
          logOrIgnore.printStackTrace();
        }
    }
 
    System.out.println(output);
  }
}

library(httr)
library(jsonlite)
library(xml2)
 
server <- "http://rest.ensembl.org"
ext <- "/sequence/id/ENSP00000288602?"
 
r <- GET(paste(server, ext, sep = ""), content_type("application/json"))
 
stop_for_status(r)
 
# use this if you get a simple nested list back, otherwise inspect its structure
# head(data.frame(t(sapply(content(r),c))))
head(fromJSON(toJSON(content(r))))

 
curl 'http://rest.ensembl.org/sequence/id/ENSP00000288602?' -H 'Content-type:application/json'

wget -q --header='Content-type:application/json' 'http://rest.ensembl.org/sequence/id/ENSP00000288602?'  -O -

Resource Information

Methods	GET
Response formats	fasta json seqxml text yaml jsonp
Slice length	1e7