restaurog

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. (PubMed)

Overview

Base URL

• http://rest.g-language.org/
• http://useG.jp/

Syntax

http://rest.g-language.org/[genome ID]/restauro

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