Ensembl Rest API - GET sequence/region/:species/:region

Returns the genomic sequence of the specified region of the given species. Supports feature masking and expand options.

Parameters

Required

Name	Type	Description	Default	Example Values
region	`String`	Query region. A maximum of 10Mb is allowed to be requested at any one time	`-`	`X:1000000..1000100:1` `X:1000000..1000100:-1` `X:1000000..1000100`
species	`String`	Species name/alias	`-`	`homo_sapiens` `human`

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`
coord_system	`String`	Filter by coordinate system name	`-`	`contig` `seqlevel`
coord_system_version	`String`	Filter by coordinate system version	`-`	`GRCh37`
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 lower cased 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`	`1`

Example Requests

/sequence/region/human/X:1000000..1000100:1?content-type=text/plain

use strict;
use warnings;

use HTTP::Tiny;

my $http = HTTP::Tiny->new();

my $server = 'https://jan2020.rest.ensembl.org';
my $ext = '/sequence/region/human/X:1000000..1000100:1?';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'text/plain' }
});

die "Failed!\n" unless $response->{success};


print "$response->{status} $response->{reason}\n";

import requests, sys

server = "https://jan2020.rest.ensembl.org"
ext = "/sequence/region/human/X:1000000..1000100:1?"

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 = "https://jan2020.rest.ensembl.org"
ext = "/sequence/region/human/X:1000000..1000100:1?"

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='https://jan2020.rest.ensembl.org'
path = '/sequence/region/human/X:1000000..1000100:1?'

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 = "https://jan2020.rest.ensembl.org";
    String ext = "/sequence/region/human/X:1000000..1000100:1?";
    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 <- "https://jan2020.rest.ensembl.org"
ext <- "/sequence/region/human/X:1000000..1000100:1?"

r <- GET(paste(server, ext, sep = ""), content_type("text/plain"))

stop_for_status(r)


print(content(r))


curl 'https://jan2020.rest.ensembl.org/sequence/region/human/X:1000000..1000100:1?' -H 'Content-type:text/plain'

wget -q --header='Content-type:text/plain' 'https://jan2020.rest.ensembl.org/sequence/region/human/X:1000000..1000100:1?'  -O -

/sequence/region/human/ABBA01004489.1:1..100?coord_system=seqlevel;content-type=text/x-fasta

use strict;
use warnings;

use HTTP::Tiny;

my $http = HTTP::Tiny->new();

my $server = 'https://jan2020.rest.ensembl.org';
my $ext = '/sequence/region/human/ABBA01004489.1:1..100?coord_system=seqlevel';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'text/x-fasta' }
});

die "Failed!\n" unless $response->{success};


print "$response->{status} $response->{reason}\n";

import requests, sys

server = "https://jan2020.rest.ensembl.org"
ext = "/sequence/region/human/ABBA01004489.1:1..100?coord_system=seqlevel"

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 = "https://jan2020.rest.ensembl.org"
ext = "/sequence/region/human/ABBA01004489.1:1..100?coord_system=seqlevel"

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='https://jan2020.rest.ensembl.org'
path = '/sequence/region/human/ABBA01004489.1:1..100?coord_system=seqlevel'

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 = "https://jan2020.rest.ensembl.org";
    String ext = "/sequence/region/human/ABBA01004489.1:1..100?coord_system=seqlevel";
    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 <- "https://jan2020.rest.ensembl.org"
ext <- "/sequence/region/human/ABBA01004489.1:1..100?coord_system=seqlevel"

r <- GET(paste(server, ext, sep = ""), content_type("text/x-fasta"))

stop_for_status(r)


print(content(r))


curl 'https://jan2020.rest.ensembl.org/sequence/region/human/ABBA01004489.1:1..100?coord_system=seqlevel' -H 'Content-type:text/x-fasta'

wget -q --header='Content-type:text/x-fasta' 'https://jan2020.rest.ensembl.org/sequence/region/human/ABBA01004489.1:1..100?coord_system=seqlevel'  -O -

/sequence/region/human/X:1000000..1000100:1?content-type=text/x-fasta;expand_5prime=60;expand_3prime=60

use strict;
use warnings;

use HTTP::Tiny;

my $http = HTTP::Tiny->new();

my $server = 'https://jan2020.rest.ensembl.org';
my $ext = '/sequence/region/human/X:1000000..1000100:1?expand_3prime=60;expand_5prime=60';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'text/x-fasta' }
});

die "Failed!\n" unless $response->{success};


print "$response->{status} $response->{reason}\n";

import requests, sys

server = "https://jan2020.rest.ensembl.org"
ext = "/sequence/region/human/X:1000000..1000100:1?expand_3prime=60;expand_5prime=60"

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 = "https://jan2020.rest.ensembl.org"
ext = "/sequence/region/human/X:1000000..1000100:1?expand_3prime=60;expand_5prime=60"

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='https://jan2020.rest.ensembl.org'
path = '/sequence/region/human/X:1000000..1000100:1?expand_3prime=60;expand_5prime=60'

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 = "https://jan2020.rest.ensembl.org";
    String ext = "/sequence/region/human/X:1000000..1000100:1?expand_3prime=60;expand_5prime=60";
    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 <- "https://jan2020.rest.ensembl.org"
ext <- "/sequence/region/human/X:1000000..1000100:1?expand_3prime=60;expand_5prime=60"

r <- GET(paste(server, ext, sep = ""), content_type("text/x-fasta"))

stop_for_status(r)


print(content(r))


curl 'https://jan2020.rest.ensembl.org/sequence/region/human/X:1000000..1000100:1?expand_3prime=60;expand_5prime=60' -H 'Content-type:text/x-fasta'

wget -q --header='Content-type:text/x-fasta' 'https://jan2020.rest.ensembl.org/sequence/region/human/X:1000000..1000100:1?expand_3prime=60;expand_5prime=60'  -O -

/sequence/region/human/X:1000000..1000100:1?content-type=application/json

use strict;
use warnings;

use HTTP::Tiny;

my $http = HTTP::Tiny->new();

my $server = 'https://jan2020.rest.ensembl.org';
my $ext = '/sequence/region/human/X:1000000..1000100:1?';
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 = "https://jan2020.rest.ensembl.org"
ext = "/sequence/region/human/X:1000000..1000100:1?"

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 = "https://jan2020.rest.ensembl.org"
ext = "/sequence/region/human/X:1000000..1000100:1?"

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='https://jan2020.rest.ensembl.org'
path = '/sequence/region/human/X:1000000..1000100:1?'

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 = "https://jan2020.rest.ensembl.org";
    String ext = "/sequence/region/human/X:1000000..1000100:1?";
    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 <- "https://jan2020.rest.ensembl.org"
ext <- "/sequence/region/human/X:1000000..1000100:1?"

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 'https://jan2020.rest.ensembl.org/sequence/region/human/X:1000000..1000100:1?' -H 'Content-type:application/json'

wget -q --header='Content-type:application/json' 'https://jan2020.rest.ensembl.org/sequence/region/human/X:1000000..1000100:1?'  -O -

/sequence/region/human/X:1000000..1000100:1?mask=soft;content-type=text/x-fasta

use strict;
use warnings;

use HTTP::Tiny;

my $http = HTTP::Tiny->new();

my $server = 'https://jan2020.rest.ensembl.org';
my $ext = '/sequence/region/human/X:1000000..1000100:1?mask=soft';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'text/x-fasta' }
});

die "Failed!\n" unless $response->{success};


print "$response->{status} $response->{reason}\n";

import requests, sys

server = "https://jan2020.rest.ensembl.org"
ext = "/sequence/region/human/X:1000000..1000100:1?mask=soft"

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 = "https://jan2020.rest.ensembl.org"
ext = "/sequence/region/human/X:1000000..1000100:1?mask=soft"

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='https://jan2020.rest.ensembl.org'
path = '/sequence/region/human/X:1000000..1000100:1?mask=soft'

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 = "https://jan2020.rest.ensembl.org";
    String ext = "/sequence/region/human/X:1000000..1000100:1?mask=soft";
    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 <- "https://jan2020.rest.ensembl.org"
ext <- "/sequence/region/human/X:1000000..1000100:1?mask=soft"

r <- GET(paste(server, ext, sep = ""), content_type("text/x-fasta"))

stop_for_status(r)


print(content(r))


curl 'https://jan2020.rest.ensembl.org/sequence/region/human/X:1000000..1000100:1?mask=soft' -H 'Content-type:text/x-fasta'

wget -q --header='Content-type:text/x-fasta' 'https://jan2020.rest.ensembl.org/sequence/region/human/X:1000000..1000100:1?mask=soft'  -O -

/sequence/region/human/X:1000000..1000100:1?content-type=text/x-fasta

use strict;
use warnings;

use HTTP::Tiny;

my $http = HTTP::Tiny->new();

my $server = 'https://jan2020.rest.ensembl.org';
my $ext = '/sequence/region/human/X:1000000..1000100:1?';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'text/x-fasta' }
});

die "Failed!\n" unless $response->{success};


print "$response->{status} $response->{reason}\n";

import requests, sys

server = "https://jan2020.rest.ensembl.org"
ext = "/sequence/region/human/X:1000000..1000100:1?"

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 = "https://jan2020.rest.ensembl.org"
ext = "/sequence/region/human/X:1000000..1000100:1?"

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='https://jan2020.rest.ensembl.org'
path = '/sequence/region/human/X:1000000..1000100:1?'

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 = "https://jan2020.rest.ensembl.org";
    String ext = "/sequence/region/human/X:1000000..1000100:1?";
    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 <- "https://jan2020.rest.ensembl.org"
ext <- "/sequence/region/human/X:1000000..1000100:1?"

r <- GET(paste(server, ext, sep = ""), content_type("text/x-fasta"))

stop_for_status(r)


print(content(r))


curl 'https://jan2020.rest.ensembl.org/sequence/region/human/X:1000000..1000100:1?' -H 'Content-type:text/x-fasta'

wget -q --header='Content-type:text/x-fasta' 'https://jan2020.rest.ensembl.org/sequence/region/human/X:1000000..1000100:1?'  -O -

Resource Information

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