Provider:
Center for Biological Sequence Analysis (CBS)
Location:
Denmark
Submitter/Source:
SeekDa (over 6 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 Login to add a documentation URL Description(s): from provider’s description doc (over 6 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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