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restaurog [2014/01/18 07:44] (current)
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 +====== REST Web Service for Restauro-G ======
 +
 +Annotations of complete genome sequences submitted directly by sequencing projects are diverse in terms of annotation strategies and update frequencies,​ and these inconsistencies make comparative study difficult. To allow rapid data preparation of a large number of complete genomes, automation and speed are important objectives for genome re-annotation. Here we introduce an open-source rapid genome re-annotation software system, Restauro-G, specialized for bacterial genomes. Restauro-G re-annotates the genome by similarity searches utilizing the BLAST-Like Alignment Tool, referring to protein databases such as UniProt Knowledgebase,​ NCBI nr, NCBI COGs, PFAM, and Psortdb. Re-annotation by Restauro-G achieved over 98% accuracy for most bacterial chromosomes in comparison with the original manually curated annotation of EMBL releases. Restauro-G was developed in the generic bioinformatics workbench G-language Genome Analysis Environment and is distributed at http://​restauro-g.iab.keio.ac.jp/​ under the GNU General Public License.
 +
 +
 +We here provide a REST service for this Restauro-G software.
 +
 +Users of this service should also consult the original documentations of Restauro-G, and cite the following article.
 +
 +  * Tamaki S, Arakawa K, Kono N, Tomita M, "​Restauro-G:​ A Rapid Genome Re-Annotation System for Comparative Genomics",​ //Genomics Proteomics Bioinformatics//,​ 2007, **5**(1): 53-58. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​17572364|(PubMed)]]
 +
 +==== Overview ====
 +== Base URL ==
 +   * http://​rest.g-language.org/​
 +   * http://​useG.jp/​
 +
 +== Syntax ==
 +<​code>​
 +http://​rest.g-language.org/​[genome ID]/​restauro
 +</​code>​
 +
 +Here the [genome ID] can by any RefSeq ID, or ID given by the REST service upon local file upload. (described later)
 +
 +== List of locally available genomes ==
 +   * http://​rest.g-language.org/​organism_list
 +
 +==== File upload ====
 +   * http://​rest.g-language.org/​upload/​
 +The uploaded file must be in GenBank format, and each CDS feature.
 +
 +== example ==
 +  * http://​rest.g-language.org/​NC_000913/​restauro ​ for //​Eshecrichia coli// K12
 +  * http://​rest.g-language.org/​NC_000964/​restauro ​ for //Bacillus subtilis//
 +
  
restaurog.txt ยท Last modified: 2014/01/18 07:44 (external edit)