TargetP 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/TargetP/examples/xml-compile.pl
wget http://www.cbs.dtu.dk/ws/TargetP/examples/targetp.pl
perl targetp.pl -P|-N [-t float] < example.fsa
Documentation
INTRODUCTION
This Web Service implements TargetP v.1.1.ws0. It predicts the
subcellular location of eukaryotic protein sequences. The assignment
is based on the predicted presence of any of the N-terminal presequences:
chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP)
or secretory pathway signal peptide (SP). The method is described in
detail in the following article:
Locating proteins in the cell using TargetP, SignalP, and related tools.
Olof Emanuelsson, Soren Brunak, Gunnar von Heijne, Henrik Nielsen
Nature Protocols 2, 953-971 (2007).
Alongside this Web Service the TargetP method is also implemented as
a traditional click-and-paste WWW server at:
http://www.cbs.dtu.dk/services/TargetP/
TargetP is also available as a stand-alone software package to install
and run at the user's site, with the same functionality. For academic
users there is a download page at:
http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?targetp
Other users are requested to write to software@cbs.dtu.dk for details.
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
* 'organism' Organism type of the input sequences (mandatory):
"P" plant;
"N" non-plant.
* 'cleavage' Include cleavage site prediction.
(no value, just presence/absence);
* 'cTP' A cutoff for predicting cTP.
The value must be between 0.0 and 1.0.
* 'SP' A cutoff for predicting SP.
The value must be between 0.0 and 1.0.
* 'mTP' A cutoff for predicting mTP.
The value must be between 0.0 and 1.0.
* 'other' A cutoff for predicting "other".
The value must be between 0.0 and 1.0.
* 'sequencedata' mulitple elements of type 'sequence':
* 'sequence' answers to one sequence:
* 'id' unique identifier for the sequence;
* 'comment' optional comment;
* 'seq' protein sequence. The sequence must be written
using the one letter amino acid code:
`acdefghiklmnpqrstvwy' or `ACDEFGHIKLMNPQRSTVWY'.
Other letters will be converted to `X' and treated
as unknown amino acids. Other symbols,
such as whitespace and numbers, will be ignored.
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: * 'annsource'
'method' name of the method, here always 'TargetP';
'version' version of the method: here always '1.1 ws0';
'ann' annotations - one element per input sequence;
'sequence' standard sequence object;
'id' sequence identifier;
'annrecords/annrecord'
'feature' feature name, here always 'TargetP';
'global' always present, indicates the whole sequence;
'score'
'key'='cTP' prediction for chloroplast transit peptide;
'value' NN prediction score for "cTP";
This score is present only for the plants.
'score'
'key'='mTP' prediction for mitochondrial targeting peptide;
'value' NN prediction score for "mTP";
'score'
'key'='SP' prediction for secretory pathway signal peptide;
'value' NN prediction score for "SP";
'score'
'key'='other' prediction for other location of the protein;
'value' NN prediction score for "other";
'score'
'key'='RC' reliability class of prediction;
'value' the value fo "RC". RC is a measure of the size of
the difference ('diff') between the highest (winning)
and the second highest output scores. There are
5 reliability classes, the lower the value of RC
the safer the prediction;
'comment' Contains answer of prediction of localization, based
on the scores above. The possible values are:
"C" - Chloroplast, i.e. the sequence contains cTP,
a chloroplast transit peptide;
"M" - Mitochondrion, i.e. the sequence contains mTP,
a mitochondrial targeting peptide;
"S" - Secretory pathway, i.e. the sequence contains SP,
a signal peptide;
"_" - Any other location;
"*" - "don't know"; indicates that cutoff restrictions
were set and the winning network output score was
below the requested cutoff for that category.
It also contains predicted presequence length if TargetP
was asked to perform cleavage site predictions.
More comprehensive information about the output could be found at:
http://www.cbs.dtu.dk/services/TargetP/output.php
CONTACT
Questions concerning the scientific aspects of the NetCTL method should
go to Olof Emanuelsson, olof@sbc.su.se; technical question concerning
the Web Service should go to Edita Bartaseviciute, edita@cbs.dtu.dk or
Kristoffer Rapacki, rapacki@cbs.dtu.dk.
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