WSEasyGene_1_0

By | September 22, 2011

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

Name
WSEasyGene_1_0
Documentation
Protocol
SOAP
WSDL
Endpoint
http://ws.cbs.dtu.dk/cgi-bin/soap/ws/server.cgi
Topic
Gene Prediction
Type
Analysis
Tags
, ,
Description

The EasyGene 1.0 server produces a list of predicted genes given a sequence of prokaryotic DNA. Each prediction is attributed [...]

Further information

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

Original source
BioCatalogue

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