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emboss

REST Service for EMBOSS (including KBWS)

EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages. (taken from EMBOSS website)

We here provide a REST service for this EMBOSS software suite as well as Keio Bioinformatics Web Services (KBWS) EMBASSY package.

Users of this service should also consult the original documentations of EMBOSS, and cite the following article.

  • Rice P., Longden I., Bleasby A. (2000). EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16, 276-7. (PubMed)

Overview

Base URL
Syntax
http://rest.g-language.org/emboss/[program]/[ID]/[option]=[value]/-[flag]/
List of available programs
Documentation of each program
example

File upload

POST your data to this URL, as file1, file2, …, file10. Then pass the rest of arguments as arg. Following is a sample code for running seqret to convert your file to genbank format.

use LWP::UserAgent;
my $ua = LWP::UserAgent->new;
my $response = $ua->post("http://rest.g-language.org/emboss/",
                         Content_Type=>'multipart/form-data',
                         Content=>[file1 => [$ARGV[0]], 'arg'=>'seqret/osformat2=genbank/-feature']
                         );
 
if ($response->is_success) {
    print $response->decoded_content;
}
else {
    die $response->status_line;
}
emboss.txt · Last modified: 2014/01/18 07:44 (external edit)