Table of Contents
REST Service for G-language System
Base URL
- http://useG.jp/ (this URL forwards to the above)
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
- http://rest.g-language.org/ecoli (G-language preset genome)
- http://rest.g-language.org/NC_000908 (NCBI RefSeq accession)
- http://rest.g-language.org/B619CD (G-language REST temporary reference id)
Genes
http://rest.g-language.org/[genome]/[gene]
examples
- http://rest.g-language.org/ecoli/recA (common gene name)
- http://rest.g-language.org/ecoli/b2699 (canonical gene name / locus tag)
- http://rest.g-language.org/ecoli/FEATURE5804 (G-language feature id)
- http://rest.g-language.org/ecoli/CDS2646 (G-language CDS id)
features
http://rest.g-language.org/[genome]/[gene]/[feature]
examples
- http://rest.g-language.org/mgen/metX/gene (gene name)
- http://rest.g-language.org/mgen/metX/translation (amino acid sequence)
- http://rest.g-language.org/mgen/*/translation (amino acid sequence of all genes)
- http://rest.g-language.org/mgen/product=glucose/product (show function of genes containing "glucose" in the product feature tag)
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
- Returns a unique reference ID for the uploaded file. You can use this ID for the rest of the analysis so that the large file is not transferred over the network.
- for example, if you received an ID of "B619CD",
- http://rest.g-language.org/B619CD (show nucleotide composition statistics)
- http://rest.g-language.org/B619CD/*/translation (show amino acid sequences of all genes)
- http://rest.g-language.org/B619CD/gcskew (gcskew analysis)
genome analysis methods
list of available analysis methods
- http://rest.g-language.org/method_list/gb (data access methods)
- http://rest.g-language.org/method_list/ (analysis methods)
Syntax
http://rest.g-language.org/[genome]/[method]/[required input (if any)]/[option1=value]/[option2=value]...
Genome data access examples
- http://rest.g-language.org/ecoli/recA/before_startcodon (5' upstream sequence of recA gene)
- http://rest.g-language.org/ecoli/before_startcodon/recA (another way for 5' upstream sequence of recA gene)
- http://rest.g-language.org/ecoli/recA/get_geneseq (nucleotide sequence of recA gene)
- http://rest.g-language.org/ecoli/get_geneseq/recA (another way for nucleotide sequence of recA gene)
- http://rest.g-language.org/ecoli/cds (get a list of all feature ids)
- http://rest.g-language.org/ecoli/*/get_geneseq/ (nucleotide sequence of all genes)
- http://rest.g-language.org/ecoli/get_geneseq/* (another way for nucleotide sequence of all genes)
Analysis methods examples
- http://rest.g-language.org/ecoli/gcskew (GC skew analysis - produces a graph)
- http://rest.g-language.org/ecoli/gcskew/cumulative=1 (cumulative GC skew)
- http://rest.g-language.org/ecoli/gcskew/at=1/cumulative=1/output=f/ (cumulative AT skew - output as csv data)
- http://rest.g-language.org/ecoli/gcsi (GC Skew Index analysis - single double value)
other methods
list of available analysis methods
Syntax
http://rest.g-language.org/[method]/[required input (if any)]/[option1=value]/[option2=value]...
Examples
- http://rest.g-language.org/togoWS/C00001 (use togoWS to retrieve data)
- http://rest.g-language.org/max/1,2,3,4,5 (maximum of given vector)
- http://rest.g-language.org/help/gcskew (manual of gcskew analysis method)
- http://rest.g-language.org/help/-g (list of available manual documentations)
- http://rest.g-language.org/pubmed/G-language (search pubmed with keyword: "G-language")