The ELM Resource Structure Filter

PASSED

This web service is useful for evaluating the location of candidate short regulatory sequences in proteins (linear motifs) which need to be accessible to interact with their ligand domains. The StructureFilter web-service calculates an accessibility score, secondary structure score and total score (as well as various other features) for each match of a regular expression or ELM in the query sequence for which structural information is available. (If a regular expression match is determined as having no associated structural information available, no reference is made to this match in the result set.)

the web service consists of three methods:

  • RunJob
  • GetStatus
  • GetResult

Reference:

A structure filter for the Eukaryotic Linear Motif Resource
Allegra Via, Cathryn M Gould, Christine Gemuend, Toby J Gibson and Manuela Helmer-Citterich
BMC Bioinformatics, 2009 (in review)

A description of the WSDL service:

StructureFilter

Namespace: http://structureFilter.embl.de/StructureFilter

This WSDL file describe the Structure Filter Web Service. It calculates an accessibility score, secondary structure score and total score(as well as various other features) for each match of a regular expression or ELM in the query sequence for which structural information is available. If a regular expression match is determined as having no associated structural information available no reference is made to this match in the result set. Via et al. 2008 http://structurefilter.embl.de/webservice/clients/structureFilterClient.txt


  • Port: StructureFilter
  • Location: http://luna.embl.de:8080/axis2/services/StructureFilter
  • Protocol: http://schemas.xmlsoap.org/soap/http
  • Default Style: document

Operations

RunJob

This operation is the initial operation in a stateful interaction with the Structure Filter service.

  • SOAP Action: http://structureFilter.embl.de/StructureFilter/RunJob
  • Input Message: RunJobMsg
    • parameters
      • RunJob type
        • identifier type string
          • querySequence type
            • restriction type string
            • regularExpression type
              • restriction type string
              • elmIdentifierName type
                • restriction type string
                • includeSecondaryStructureRecords type
                  • restriction type string
                  • includeAccessibilityRecords type
                    • restriction type string
              • Output Message: RunJobResponseMsg
                • parameters
                  • RunJobResponse type
                    • JobIdentifier type string

                GetStatus

                This operation returns the status of a job identified by its job identifier. A client should use this operation to be aware when/if the results are available.

                • SOAP Action: http://structureFilter.embl.de/StructureFilter/GetStatus
                • Input Message: GetStatusMsg
                  • parameters
                    • GetStatus type
                      • JobIdentifier type string
                  • Output Message: GetStatusResponseMsg
                    • parameters
                      • GetStatusResponse type
                        • Status type string
                          • StatusDetails type string
                      • Fault Message: JobIdentifierFaultMsg
                        • fault
                          • JobIdentifierFault type
                            • FaultDescription type string

                        GetResult

                        This operation returns the resulting predictions.

                        • SOAP Action: http://structureFilter.embl.de/StructureFilter/GetResult
                        • Input Message: GetResultMsg
                          • parameters
                            • GetResult type
                              • JobIdentifier type string
                          • Output Message: GetResultResponseMsg
                            • parameters
                              • GetResultResponse type
                                • sequence type SequenceType
                                  • identifier type
                                    • restriction type string
                                    • sequence type
                                      • restriction type string
                                    • structureFilterRecord type StructureFilterRecordType
                                      • ELMIdentifier type string
                                        • regularExpression type string
                                          • start type integer
                                            • end type integer
                                              • accessibilityScore type decimal
                                                • accessibilityScorePValue type decimal
                                                  • secondaryStructureScore type decimal
                                                    • secondaryStructureScorePValue type decimal
                                                      • totalScore type decimal
                                                        • totalScorePValue type decimal
                                                          • targetDomainStructure type string
                                                            • percentageIdentity type decimal
                                                              • benchmarkAssignment type string
                                                                • individualResidueValues type IndividualResidueValuesType
                                                                  • position type integer
                                                                    • targetDomainStructure type string
                                                                      • accessibility type decimal
                                                                        • secondaryStructure type string
                                                                      • secondaryStructureRecord type SecondaryStructureRecordType
                                                                        • start type integer
                                                                          • end type integer
                                                                            • secondaryStructure type string
                                                                              • targetDomainStructure type string
                                                                              • accessibilityRecord type AccessibilityRecordType
                                                                                • position type integer
                                                                                  • accessibility type decimal
                                                                                    • targetDomainStructure type string
                                                                              • Fault Message: JobIdentifierFaultMsg
                                                                                • fault
                                                                                  • JobIdentifierFault type
                                                                                    • FaultDescription type string

                                                                                WSDL Changes

                                                                                DateDescription of Changes
                                                                                22nd April 2009First Snapshot
                                                                                PASSED

                                                                                Test #1: StructureFilter_test

                                                                                The StructureFilter web-service consists of the following three methods:

                                                                                • RunJob
                                                                                • GetStatus
                                                                                • GetResult

                                                                                the runStructureFilterWS.py script tests the functionality of all three methods of this web-service.
                                                                                The results from the Strucuture Filter web-service are deterministic so the script checks for exact values for the output.

                                                                                Great Articles………….. thank

                                                                                for each match of a regular

                                                                                for each match of a regular expression or ELM in the query sequence for which structural information is available. If a regular expression match is determined as having no associated structural information available no reference is made to this match.
                                                                                Download Youtube Videos()Download Roms

                                                                                Auto Insurance Health

                                                                                This operation returns the

                                                                                This operation returns the status of a job identified by its job identifier. A client should use this operation to be aware when/if the results are available.
                                                                                Electronic Cigarette Reviews()Blu Cigs E-Cigarette

                                                                                I also like Selena Gomez and

                                                                                I also like Selena Gomez and Demi Lovato. favs r color black food fruit and animal cat book a bunch of them ..Nice to see u back........

                                                                                Small Business Grants | Logo Design Services

                                                                                Mais comme nous sommes entrés

                                                                                Mais comme nous sommes entrés dans l'âge mûr, nous avons commencé 000-200 réaliser que beaucoup de notre temps était consacré précipitent pour garder tous ces plaques en l'air. Nous avions pris tant 1z0-052 d'obligations, il se sentait parfois comme si nous étions esclaves de fatigante et stressante attentes, des déceptions et les galères. Nous étions devenus si occupés à garder tous nos assiettes dans l'air que nous avons à peine eu le temps ni l'énergie 70-448 pour nourrir nous-mêmes et nos proches.

                                                                                Thank for sharing

                                                                                wanted to say that I have

                                                                                wanted to say that I have really enjoyed reading your blog posts. Any way I'll be subscribing to your feed and I hope you post again soon
                                                                                e card design | menu navigation design | small business website | | website header design

                                                                                THANKS for the information

                                                                                THANKS for the information I love Ashley Tisdale , love her style of music and clothing,love all her songs,and she one of my favorite singers. I also like Selena Gomez and Demi Lovato. favs r color black food fruit and animal cat book a bunch of them and a lot more. im a shy person and please coment!! THANKS!!!!!! also uuuummmm ha ha ha i wasnt gona say anyting!!! wow tat was the most retarted ting ever. oh who cares whos sees tis?! (lik a millon peps dummy!)
                                                                                web banner design