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REST Service for G-language System

G-language Genome Analysis Environment (G-language GAE) is a set of Perl libraries for genome sequence analysis that is compatible with BioPerl, equipped with several software interfaces (interactive Perl/UNIX shell with persistent data, AJAX Web GUI, Perl API). The software package contains more than 100 original analysis programs especially focusing on bacterial genome analysis, including those for the identification of binding sites with information theory, analysis of nucleotide composition bias, analysis of the distribution of characteristic oligonucleotides, analysis of codons and prediction of expression levels, and visualization of genomic information. Taking advantage of the BioHackathon 2009, we have recently developed REST/SOAP web service APIs for this software system, in order to provide higher interoperability with other programming languages and bioinformatics software tools.

REST interface provides RESTful URL-based access to all functions of G-language GAE, which is highly interoperable to be accessed from other online resources. Here all analysis resource can be accessed through HTTP GET/POST request using unique URI. For example, graphical result of the GC skew analysis of Escherichia coli K12 genome is given by http://rest.g-language.org/NC_000913/gcskew, and cumulative GC skew analysis is given by http://rest.g-language.org/NC_000913/gcskew/cumulative=1/. Therefore, biological web sites can embed these analyses simply by linking to these URLs. These URLs gives the graphical results very quickly, but the analysis is done on the server on the fly, and the results are dynamics. This speed is a good example of the high performance of G-language System.

The web service API is already utilized in several software tools, including a lightweight version of G-language System available at CPAN that functions as a wrapper around the REST services, with minimal number of external modules for easy installation, and with minimal computational resource requirement. A web service for the generation of interactive and zoomable Chaos Game Representation images is also available utilizing the REST service.

Base URL
List of available methods
Publication
  • "G-language genome analysis environment with REST and SOAP web service interfaces", Arakawa K, Kido N, Oshita K, Tomita M, Nucleic Acids Res., 2010, 38 Suppl:W700-705 (PubMed).

genome flatfile access

list of available genomes

Syntax

http://rest.g-language.org/[genome]/[gene]/[feature]
Genomes (nucleotide composition)
http://rest.g-language.org/[genome]
examples
Genes
http://rest.g-language.org/[genome]/[gene]
examples
features
http://rest.g-language.org/[genome]/[gene]/[feature]
examples

file upload

Base URL
Syntax
  • POST a file to fileform=file
  • File types are automatically interpreted by the system. Supported formats are: ABI, ACE, ALF, BSML, CTF, EMBL, Entrez Gene, Exp, FastA, FastQ, GCG, GenBank, Phd, PIR, PLN, raw, SCF, SWISS.
Return

genome analysis methods

list of available analysis methods
Syntax
http://rest.g-language.org/[genome]/[method]/[required input (if any)]/[option1=value]/[option2=value]...
Genome data access examples
Analysis methods examples

other methods

list of available analysis methods
Syntax
http://rest.g-language.org/[method]/[required input (if any)]/[option1=value]/[option2=value]...
Examples
rest.txt · Last modified: 2014/01/18 16:44 (external edit)