restauro

Restauro-G version 2

Restauro-G version 2 is a rapid data "broker" service that collects and adds related information to a given gene (or gene set).

Re-annotation is an essential step as a basis for comparative analyses, in order to collect up-to-date information under standardized criteria, with certain syntax and semantics for effective computational handling. For this purpose, a rapid, automatic, and high-quality genome re-annotation system is desirable. Such annotation “broker” service would also be useful in linking resources that are disparsed in several databases.

Single gene mode collects cross-references information related with a given gene ID or sequence, and returns as useful formats. When ID converting is failed or query is sequence (nucleotide or amino acid), this system tries ID matching by similarity search with BLAT to Swiss-Prot and TrEMBL. Therefore, this system meets demand for high-performance ID converter and overlooking functions, products, and features target genes.

Whole genome mode re-annotates all of genes included in genome file with "Single gene mode". Steps of data preparation for analysis have to be rapid, automatic, and high-quality. This system can get genome data as general format (GenBank file, EMBL file, RefSeq ID, or EMBL ID), gather cross-references information with method of "Single gene mode", and returns useful format (GenBank or EMBL format).

Base URL

• http://rest.g-language.org/annotation/
• http://useG.jp/annotation/ (this URL forwards to the above)

Document (Japanese)

• Japanese document is available from here.

Usage

Restauro-G version 2 is provided by REST interface. Database cross-references information related as given gene ID or sequence (nucleotide or amino acid) can be accessed through HTTP GET/POST request using unique URI.

REST URI conventions

• http://rest.g-language.org/annotation/[GENE](/options)
• http://useG.jp/annotation/[GENE](/options)

Qualifiers

Standard qualifiers

• GENE * Sequence (nucleotide or amino acid) * Gene ID (Available ID list is here)

Optional qualifiers

• /format=[FORMAT]

  • out (Tabular)
  • nt (Notation3)
  • rdf (RDF)
  • html (HTML)

• /filter=[FILTER]

  • Available filter list is here.

• /evalue=[E-VALUE THRESHOLD]

  • default: /evalue=1e-70
  • E-value threshold for similarity search by BLAT against Swiss-Prot
  • This option is valid only user given sequence data to GENE

• /identity=[IDENTITY THRESHOLD]

  • default: /identity=0.98
  • Identity threshold for similarity search by BLAT against Swiss-Prot
  • This option is valid only user given sequence data to GENE)

• /direct=0

  • if "/direct=1", this service shows related information about top-hit Uniprot ID (feeling lucky)

Usage Examples

• http://rest.g-language.org/annotation/GeneID:947170

  • Related information to GeneID:947170 as tabular format.

• http://rest.g-language.org/annotation/eco:b2699/format=nt/filter=GOslim

  • GO slim about eco:b2699 (KEGG Gene) as N-Triple format.

• http://rest.g-language.org/annotation/MMQESATETISNSSMNQNGMSTLSSQLD...

  • Information table about UniProt IDs which is reported by BLAT search about given AminoSeq against Swiss-Prot.
  • https://gist.github.com/1172846
  • Perl script to get related information to top-hit UniProt ID by BLAT search against Swiss-Prot.

Quick Start

Input sequence (Amino acid or Nucleotide) or Gene ID
<textarea name="query" cols="80" rows="5"> </textarea>

Output Format
Tabular (default) Notation3 RDF
Offset value
only ID Mapping (does not perform sequence similarity search) <option value="1" selected> Swiss-Prot level 1,2 (default) </option> <option value="2"> Swiss-Prot and TrEMBL level 1,2 </option> <option value="3"> Swiss-Prot and TrEMBL level 1~4 </option> <option value="4"> Swiss-Prot and TrEMBL level 1~5 (all) </option> </select> </p> <br /> <input type="submit" /> </form>