Web Service WSEasyGene_1_0 SOAP Dk

Cog_error Archived / Deprecated

This service has been archived because it may not be active anymore (or is close to being non active). Please do not use it as it may not be accessible.

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Annotations: 13 Total number of annotations from the provider's definition / description document. 1 Total number of annotations submitted by members of BioCatalogue. 8 Total number of annotations sourced from other registries. 4

Overview

Provider:
Center for Biological Sequence Analysis (CBS)

Location:
Denmark Dk

Submitter/Source:
SeekDa (over 11 years ago)

Base URL:
http://ws.cbs.dtu.dk/cgi-bin/soap/ws/server.cgi

WSDL Location:
http://www.cbs.dtu.dk/ws/EasyGene/EasyGene_1_0.wsdl (download last cached WSDL file)

Documentation URL(s):
None
Description(s):
from provider's description doc (over 11 years ago)
The EasyGene 1.0 server produces a list of predicted genes given a sequence of prokaryotic 
DNA. Each prediction is attributed with a significance score (R-value) indicating how likely 
it is to be just a non-coding open reading frame rather than a real gene. The user needs 
only to specify the organism hosting the query sequence. Two more parameters (start codon 
leniency and R-value cutoff) have default values which may be altered if needed.

	http://www.cbs.dtu.dk/services/EasyGene/

This service is fully asynchronous;  the usage is split into the following
three operations, which is usually executed in this order.

Procedures and messages used are either common and shared among all the CBS
Web Services, or distinct to each individual Web Service. Marked [distinct] and
[common] respectively.

1. runService [distinct/common]
	Submit the input parapeter(s) and sequence data and returns a job identifier

	Input: [distinct]
				* 'startCodonLeniency' - Start codon leniency, 0/1/2 (default 0)
				* 'Rvalue' - R-value cutoff (default 2)
				* 'logOdds' - LogOdds cutoff (default -10)
				* 'model' - Organism abbreviation for model:
				                aerpe: Aeropyrum pernix
				                bacan: Bacillus anthracis
				                bachd: Bacillus halodurans
				                bacsu: Bacillus subtilis
				                biflo: Bifidobacterium longum
				                borbu: Borrelia burgdorferi 
				                brume: Brucella melitensis
				                brusu: Brucella suis
				                camje: Campylobacter jejuni
				                caucr: Caulobacter crescentus
				                chltr: Chlamydia trachomatis 
				                ecoli: Escherichia coli K-12
				                haein: Haemophilus influenzae
				                helpj: Helicobacter pylori J-99
				                hybut: Hyperthermus butylicus
				                lacla: Lactococcus lacti
				                myctu: Mycobacterium tuberculosis
				                mycge: Mycoplasma genitalium
				                oceih: Oceanobacillus iheyensis
				                ricpr: Rickettsia prowazekii
				                salti: Salmonella typhi
				                staan: Staphylococcus aureus
				                sulac: Sulfolobus acidocaldarius
				                sulso: Sulfolobus solfataricus
				                sulto: Sulfolobus tokodaii
				                thema: Thermotoga maritima
				                vibrio: Vibrio cholerae
				* 'sequences' - An array of sequence objects, containing the following elements:
				 *  'ident' - The identifier of the sequence
				 *  'seq' - The sequence specified as one continous string
	Output: [common]
				* 'jobid' - The 32 byte identification string of the job
				* 'datetime' - The last timepoint at which the status of the job has changed
				* 'status' - Possible values are QUEUED, ACTIVE, FINISHED, WAITING, REJECTED, 
				  UNKNOWN JOBID or QUEUE DOWN
	
2. pollQueue [common]
Once obtained from 'runService', a job identification can be used to poll the
status to see if the result is ready for download.

	Input:   [common]
				* 'jobid' - The 32 byte identification string of the job
	Output:  [common]
				* 'jobid' - The 32 byte identification string of the job
				* 'datetime' - The last timepoint at which the status of the job has changed
				* 'status' - Possible values are QUEUED, ACTIVE, FINISHED, WAITING, REJECTED, 
				  UNKNOWN JOBID or QUEUE DOWN

3. fetchResult  [distinct/common]
Once the status is 'FINISHED' the results generated by the Web Service can be retrieved by
specifying the jobid;

	Input:   [common]
				* 'jobid' - The 32 byte identification string of the job
	Output:  [distinct]
				*  'predictionTitle' - Short description of the generated output
				*  'predictor' - Name and version of the program which generated the output
				*  'reference' - Publication / reference of the method
				*  'predictionDate' - Date at the time the when the prediction finished
				*  'entries' - A collection of gene predictions containing the following information:
				 *    'sequence' - The sequence name
				 *    'feature' - Feature type (CDS)
				 *    'begin' - Start position of the gene (integer)
				 *    'end' - stop position of the gene (integer)
				 *    'Rvalue' - R-value for the prediction
				 *    'strand' - strand of the gene (+/-)
				 *    'start' - Start codon
				 *    'logOdds' - The log odds score
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