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emboss [2012/08/29 17:27]
admin [Overview]
emboss [2014/01/18 07:44]
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-====== 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. 
- 
-  * EMBOSS Project home: http://​emboss.sourceforge.net 
-  * KBWS: http://​www.g-language.org/​kbws/​ 
- 
-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. ([[http://​www.ncbi.nlm.nih.gov/​pubmed/​10827456|PubMed]]) 
- 
-==== Overview ==== 
-== Base URL == 
-   * http://​rest.g-language.org/​emboss/​ 
-   * http://​useG.jp/​emboss/ ​ (this URL forwards to the above) 
- 
-== Syntax == 
-<​code>​ 
-http://​rest.g-language.org/​emboss/​[program]/​[ID]/​[option]=[value]/​-[flag]/​ 
-</​code>​ 
- 
-== List of available programs == 
-   * http://​rest.g-language.org/​emboss/​wossname ​ 
- 
-== Documentation of each program == 
-   * http://​rest.g-language.org/​tfm/​[program] 
- 
-== example == 
-  * http://​rest.g-language.org/​emboss/​entret/​swissprot:​RECA_ECOLI/​ 
-  * [[http://​rest.g-language.org/​emboss/​seqret/​swissprot:​P53_*/​]] 
-  * http://​rest.g-language.org/​emboss/​prettyplot/​swissprot:​RECA_ECOLI/​ 
-  * [[http://​rest.g-language.org/​emboss/​emma/​swissprot:​P53_*/​]] 
- 
-==== File upload ==== 
-   * http://​rest.g-language.org/​emboss/​ 
-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. 
- 
-<code perl> 
-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;​ 
-} 
-</​code>​ 
- 
- 
- 
  
emboss.txt ยท Last modified: 2014/01/18 07:44 (external edit)