NetNES 1.1.ws0Template service
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We recommend that the first time users should load the WSDL file above
to SoapUI and investigate the Web Service operations in that environment.
SoapUI is a desktop application for inspecting, invoking, developing and
functional/load/compliance testing of Web Services over HTTP. It can be
downloaded free of charge from http://www.soapui.org/.
Examples of client side scripts using the service
Usage
# download the required scripts
wget http://www.cbs.dtu.dk/ws/NetNES/examples/xml-compile.pl
wget http://www.cbs.dtu.dk/ws/NetNES/examples/netnes.pl
perl netnes.pl < example.fsa
Documentation
INTRODUCTION
This Web Service implements NetNES v. 1.1.ws0. It predicts leucine-rich nuclear export signals (NES)
in eukaryotic proteins using a combination of neural networks and hidden Markov models.
The method is described in detail in the following article:
Analysis and prediction of leucine-rich nuclear export signals
Tanja la Cour, Lars Kiemer, Anne Molgaard, Ramneek Gupta, Karen Skriver and Soren Brunak
Protein Eng. Des. Sel., 17(6):527-36, 2004.
Alongside this Web Service the NetNES method is also implemented as
a traditional paste-and-click WWW server at:
http://www.cbs.dtu.dk/services/NetNES/
The traditional server offers extended functionality and comprehensive
documentation. It is suitable for close investigation of few proteins;
this service is recommended for high throughput projects.
WEB SERVICE OPERATION
This Web Service is fully asynchronous; the usage is split into the
following three operations:
1. runService
Input: The following parameters and data
* 'sequenceRecord' answers to one sequence:
* 'sequence' protein sequence. The sequence must be written
using the one letter amino acid code in capital letters:
`ACDEFGHIKLMNPQRSTVWY'.Other letters will be converted
to `X' and treated as unknown amino acids. Other symbols,
such as whitespace and numbers, will be ignored;
* 'customNote' optional comment;
* 'formalReference'
* 'accession' unique identifier for the sequence.
Output: Unique job identifier
2. pollQueue
Input: Unique job identifier
Output: 'jobstatus' - the status of the job
Possible values are QUEUED, ACTIVE, FINISHED, WAITING,
REJECTED, UNKNOWN JOBID or QUEUE DOWN
3. fetchResult
Input: Unique job identifier of a FINISHED job
Output: * 'annotatedSequence' annotations - one element per input sequence;
* 'sequenceRecord' answers to one sequence:
* 'sequence' protein sequence given as an input;
* 'formalReference'
* 'accession' unique identifier for the input sequence;
* 'annotation'
* 'feature'
* 'name' feature name, here always 'NetNES';
* 'occurence' occurence of a feature in a sequence;
* 'position' always present, indicates the position of each residue;
* 'point' residues number;
* 'evidence'
* 'predicted'
* 'methodId' id composed of today's day, name and version of the method.
Example: 6-4-2010NetNES-1.1ws0;
* 'score'
* 'type' = 'ANN' Artificial Neural Network (ANN) score type;
* 'value' ANN prediction score value;
* 'type' = 'HMM' Hidden Markov Model (HMM) score type;
* 'value' HMM prediction score value;
* 'type' = 'NES' NES score type - the main prediction score, calculated from ANN and HMM scores;
* 'value' NES prediction score value;
* 'verdict' contains 'Present' if the NES score exceeds the threshold, indicating that particular residue is
expected to participate in a nuclear export signal. Otherwise contains 'Impossible'.
Please note, that input and output data types of the NetNES v. 1.1.ws0 Web Service
are defined by the external canonical XML-Schema - BioXSD.
CONTACT
Technical questions concerning the Web Service
should go to Edita Bartaseviciute,edita@cbs.dtu.dk
or Kristoffer Rapacki, rapacki@cbs.dtu.dk.
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