MultAlin multiple alignment (CNRS IBCP)

260

Service version1.0

Contributor URLhttps://gbio-pbil.ibcp.fr/ws

WSDL URLhttp://gbio-pbil.ibcp.fr/media/wsdl/MultalinWS.wsdl FAILED

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WS-I Compliance Errors/Warnings

ERRORS:

WSDL definition does not conform to the schema located at http://schemas.xmlsoap.org/wsdl/soap/2003-02-11.xsd for some element using the WSDL-SOAP binding namespace, or does not conform to the schema located at http://schemas.xmlsoap.org/wsdl/2003-02-11.xsd for some element using the WSDL namespace.

WARNINGS:

Exception:org.xml.sax.SAXException: Error: cvc-complex-type.2.3: Element 'portType' cannot have character [children], because the type's content type is element-only.at org.wsi.xml.XMLUtils$ErrHandler.error(XMLUtils.java:1128)at org.apache.xerces.util.ErrorHandlerWrapper.error(Unknown Source)at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)at org.apache.xerces.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(Unknown Source)at org.apache.xerces.impl.xs.XMLSchemaValidator.reportSchemaError(Unknown Source)at org.apache.xerces.impl.xs.XMLSchemaValidator.elementLocallyValidComplexType(Unknown Source)at org.apache.xerces.impl.xs.XMLSchemaValidator.elementLocallyValidType(Unknown Source)at org.apache.xerces.impl.xs.XMLSchemaValidator.processElementContent(Unknown Source)at org.apache.xerces.impl.xs.XMLSchemaValidator.handleEndElement(Unknown Source)at org.apache.xerces.impl.xs.XMLSchemaValidator.endElement(Unknown Source)at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown Source)at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)at org.wsi.xml.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:148)at org.wsi.xml.XMLUtils.parseXML(XMLUtils.java:585)at org.wsi.xml.XMLUtils.parseXMLDocument(XMLUtils.java:173)at org.wsi.test.profile.validator.impl.wsdl.BP2703.validate(BP2703.java:88)at org.wsi.test.profile.validator.impl.BaseValidatorImpl.processAssertions(BaseValidatorImpl.java:319)at org.wsi.test.profile.validator.impl.wsdl.WSDLValidatorImpl.processDefinitionAssertions(WSDLValidatorImpl.java:592)at org.wsi.test.profile.validator.impl.wsdl.WSDLValidatorImpl.validate(WSDLValidatorImpl.java:182)at org.wsi.test.analyzer.BasicProfileAnalyzer.validateWSDL(BasicProfileAnalyzer.java:376)at org.wsi.test.analyzer.BasicProfileAnalyzer.validateConformance(BasicProfileAnalyzer.java:209)at net.embraceregistry.wsianalyzer.WsiAnalyzerExecutionImpl.executeAnalyzer(WsiAnalyzerExecutionImpl.java:288)at net.embraceregistry.wsianalyzer.ExecuateAnalyzer.main(ExecuateAnalyzer.java:25)

Description

Global multiple alignment of several sequences of proteins with the MultAlin algorithm.

Usage

You need to provide the following input arguments to the service:

“Sequences” : the set of sequences of proteins to align. These sequences must be stored in Pearson-Fasta format

The outputs of the service are:

“Status”: the status of the query
“JobId”: the JobId in the remote service environment
“Alignement”: the aligment of the query sequences generated with the ClustalW algorithm

More help about the usage of this Web service can be find on the IBCP Web Services home at http://gbio-pbil.ibcp.fr/ws

A description of the WSDL service:

Multalin_Service

Namespace: http://gbio.ibcp.fr:8090/Multalin_Service

Multalin @ IBCP (http://gbio-pbil.ibcp.fr)

Port: MultalinPort
Location: http://gbio.ibcp.fr:8090/Multalin_Service
Protocol: http://schemas.xmlsoap.org/soap/http
Default Style: rpc

Operations

submitMultalin

Submit a sequence an get a jobID

SOAP Action: urn:MultalinWS.wsdl#submitMultalin
Input Message: submitMultalinRequest
- Sequences
  - string
Output Message: submitMultalinResponse
- JobId
  - string

checkStatusMultalin

Submit a jobID and get the status

SOAP Action: urn:MultalinWS.wsdl#checkStatusMultalin
Input Message: checkStatusMultalinRequest
- JobId
  - string
Output Message: checkStatusMultalinResponse
- Status
  - string

getResultsMultalin

When job is finish, submit a jobid and get the results

SOAP Action: urn:MultalinWS.wsdl#getResultsMultalin
Input Message: getResultsMultalinRequest
- JobId
  - string
Output Message: getResultsMultalinResponse
- Clu
  - string
- Cl2
  - string
- Msf
  - string
- Logout
  - string

cancelMultalin

When some thing is wrong, cancel your job

SOAP Action: urn:MultalinWS.wsdl#cancelMultalin
Input Message: cancelMultalinRequest
- JobId
  - string
Output Message: cancelMultalinResponse
- Status
  - string

WSDL Changes

Date	Description of Changes
8th April 2009	First Snapshot

Test #1: Multalin functionnal test

Run a multiple alignment
and check the result against a pre-defined control

Submitted by cblanchet on Tue, 01/13/2009 - 16:59

Repeat pattern unit. This has

Submitted by alex25 on Sat, 05/08/2010 - 07:14.

Repeat pattern unit. This has the form : max>repeat (pattern) range>min, where min and max are integers defining the minimum and maximum number of pattern repeats 642-145 dumps and range is a range pattern unit (see above) fixing the accepted distance between two repeats. In this case the repeat pattern (e.g. 642-975 dumps a stem-loop structure) has, in general, a different nucleotide sequence. HP0-S24 dumps To search for exact repeats, i.e. with a sequence identical to that of the first matching repeat element, JN0-331 dumps the operator frepeat has to be used instead. For example the syntax: 20>frepeat (p1=NNN) 0…0>10 defines a sequence string of 11–19 identical tandem trinucleotides.