WSNetPhos_3_1b

By | September 22, 2011

INTRODUCTION

This Web Service implements NetPhos 3.1b. It predicts serine, threonine
and tyrosine phosphorylation sites in eukaryotic proteins using ensembles
of neural networks. Both generic and kinase specific predictions are
performed. The method is described in detail in the following articles.

Generic predictions:

“Sequence and structure-based prediction of eukaryotic protein
phosphorylation sites”.
Blom N, Gammeltoft S, Brunak S (1999).
J Mol Biol. 1999 Dec 17;294(5):1351-62.

Kinase specific predictions:

“Prediction of post-translational glycosylation and phosphorylation
of proteins from the amino acid sequence”.
Blom N, Sicheritz-Ponten T, Gupta R, Gammeltoft S, Brunak S (2004).
Proteomics. 2004 4(6):1633-49. Review.

Alongside this Web Service the NetPhos method is also implemented as
two traditional paste-and-click WWW servers at:

http://www.cbs.dtu.dk/services/NetPhos/ (generic predictions)
http://www.cbs.dtu.dk/services/NetPhosK/ (kinase specific predictions)

The traditional servers offer more detailed output (graphics), extended
functionality and comprehensive documentation. They are suitable for
close investigation of few proteins; this service is recommended for high
throughput projects.

NetPhos 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?netphos

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: An object of the type ‘sequencedata’ (see the complete definition
in http://www.cbs.dtu.dk/ws/common/ws_common_1_0b.xsd) holding
protein sequences with mandatory unique identifiers. Each
‘sequence’ is a pair of ‘id’ (identifier) and ‘seq’ (sequence
itself). The sequences must be written in 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: An object of the type ‘anndata’ (see the complete definition
in http://www.cbs.dtu.dk/ws/common/ws_common_1_0b.xsd) holding
the predition results. ‘annsource’ states the ‘method’ (in
this case always ‘netphos’) and ‘version’ (in this case 3.1b).
The objects of the type ‘annrecord’ hold the predictions for
a given residue in a given sequence, the fields are:

feature – active kinase (‘unsp’ for generic predictions);
pos – sequence residue;
score – prediction score, if higher than 0.5 the residue
is a predicted phosphorylation site, the higher
the score the more secure the prediction;
comment – appears only when the score is higher than 0.5,
contains the word ‘YES’.

CONTACT

Questions concerning the scientific aspects of the NetPhos method should
go to Thomas Sicheritz, thomas@cbs.dtu.dk; technical questions concerning
the Web Service should go to Peter Fischer Hallin, pfh@cbs.dtu.dk or
Kristoffer Rapacki, rapacki@cbs.dtu.dk.

Name
WSNetPhos_3_1b
Documentation
Protocol
SOAP
WSDL
Endpoint
http://ws.cbs.dtu.dk/cgi-bin/soap/ws/simple.cgi
Topic
Gene Prediction, Protein Structure Prediction
Type
Analysis
Tags
, , , , , , , , ,
Description

INTRODUCTION This Web Service implements NetPhos 3.1b. It predicts serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins using ensembles [...]

Further information

INTRODUCTION

This Web Service implements NetPhos 3.1b. It predicts serine, threonine
and tyrosine phosphorylation sites in eukaryotic proteins using ensembles
of neural networks. Both generic and kinase specific predictions are
performed. The method is described in detail in the following articles.

Generic predictions:

“Sequence and structure-based prediction of eukaryotic protein
phosphorylation sites”.
Blom N, Gammeltoft S, Brunak S (1999).
J Mol Biol. 1999 Dec 17;294(5):1351-62.

Kinase specific predictions:

“Prediction of post-translational glycosylation and phosphorylation
of proteins from the amino acid sequence”.
Blom N, Sicheritz-Ponten T, Gupta R, Gammeltoft S, Brunak S (2004).
Proteomics. 2004 4(6):1633-49. Review.

Alongside this Web Service the NetPhos method is also implemented as
two traditional paste-and-click WWW servers at:

http://www.cbs.dtu.dk/services/NetPhos/ (generic predictions)
http://www.cbs.dtu.dk/services/NetPhosK/ (kinase specific predictions)

The traditional servers offer more detailed output (graphics), extended
functionality and comprehensive documentation. They are suitable for
close investigation of few proteins; this service is recommended for high
throughput projects.

NetPhos 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?netphos

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: An object of the type ‘sequencedata’ (see the complete definition
in http://www.cbs.dtu.dk/ws/common/ws_common_1_0b.xsd) holding
protein sequences with mandatory unique identifiers. Each
‘sequence’ is a pair of ‘id’ (identifier) and ‘seq’ (sequence
itself). The sequences must be written in 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: An object of the type ‘anndata’ (see the complete definition
in http://www.cbs.dtu.dk/ws/common/ws_common_1_0b.xsd) holding
the predition results. ‘annsource’ states the ‘method’ (in
this case always ‘netphos’) and ‘version’ (in this case 3.1b).
The objects of the type ‘annrecord’ hold the predictions for
a given residue in a given sequence, the fields are:

feature – active kinase (‘unsp’ for generic predictions);
pos – sequence residue;
score – prediction score, if higher than 0.5 the residue
is a predicted phosphorylation site, the higher
the score the more secure the prediction;
comment – appears only when the score is higher than 0.5,
contains the word ‘YES’.

CONTACT

Questions concerning the scientific aspects of the NetPhos method should
go to Thomas Sicheritz, thomas@cbs.dtu.dk; technical questions concerning
the Web Service should go to Peter Fischer Hallin, pfh@cbs.dtu.dk or
Kristoffer Rapacki, rapacki@cbs.dtu.dk.

Original source
BioCatalogue

Leave Your Comment

Your email will not be published or shared. Required fields are marked *

*

*

You may use these HTML tags and attributes: <a href="" title=""> <abbr title=""> <acronym title=""> <b> <blockquote cite=""> <cite> <code> <del datetime=""> <em> <i> <q cite=""> <strike> <strong>