WSSignalP_3_0

By | September 22, 2011

INTRODUCTION

This Web Service implements SignalP v. 3.0. It predicts the presence and
location of signal peptide cleavage sites in amino acid sequences from
different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes,
and eukaryotes. The method incorporates a prediction of cleavage sites and
a signal peptide/non-signal peptide prediction based on a combination of
several artificial neural networks and hidden Markov models. The method is
described in detail in the following article:

Improved prediction of signal peptides: SignalP 3.0.
J D Bendtsen, H Nielsen, G v Heijne and S Brunak.
J. Mol. Biol., 340:783-795, 2004.

Alongside this Web Service the SignalP method is also implemented as
a traditional click-and-paste WWW server at:

http://www.cbs.dtu.dk/services/SignalP/

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

SignalP is also available as a stand-alone software package; 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
“euk” eukaryotes
“gram-” Gram-negative prokaryotes
“gram+” Gram-positive prokaryotes

* ‘method’ – prediction method
“nn” neural network only
“hmm” hidden Markov models only
“nn+hmm” both methods (the default)

* ‘sequences’ – protein sequences, with unique identifiers
The sequences 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.
All the input sequences are truncated to 70 aa from the N-terminal.
At most 2,000 sequences and 200,000 amino acids per submission;
each sequence not more than 6,000 amino acids.

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: ‘output’ – prediction results
For each input residue a record is output consisting of the
following fields:

seqname sequence name
source “signalp-3.0-nn” or “signalp-3.0-hmm” (fixed string)
feature “signal” (fixed string)
start,end predicted position of the signal peptide in the
sequence (0-0 is no peptide is predicted)
score prediction score (D score, see the article)
strand,frame N/A
comment answer (“Y” or “S” for yes, “n” or “Q” for no)

CONTACT

Questions concerning the scientific aspects of the SignalP method should go
to Henrik Nielsen, hnielsen@cbs.dtu.dk; technical question concerning the
Web Service should go to Peter Fischer Hallin, pfh@cbs.dtu.dk or Kristoffer
Rapacki, rapacki@cbs.dtu.dk.

Name
WSSignalP_3_0
Documentation
Protocol
SOAP
WSDL
Endpoint
http://ws.cbs.dtu.dk/cgi-bin/soap/ws/server.cgi
Topic
Biology
Type
Tags
, ,
Description

INTRODUCTION This Web Service implements SignalP v. 3.0. It predicts the presence and location of signal peptide cleavage sites in [...]

Further information

INTRODUCTION

This Web Service implements SignalP v. 3.0. It predicts the presence and
location of signal peptide cleavage sites in amino acid sequences from
different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes,
and eukaryotes. The method incorporates a prediction of cleavage sites and
a signal peptide/non-signal peptide prediction based on a combination of
several artificial neural networks and hidden Markov models. The method is
described in detail in the following article:

Improved prediction of signal peptides: SignalP 3.0.
J D Bendtsen, H Nielsen, G v Heijne and S Brunak.
J. Mol. Biol., 340:783-795, 2004.

Alongside this Web Service the SignalP method is also implemented as
a traditional click-and-paste WWW server at:

http://www.cbs.dtu.dk/services/SignalP/

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

SignalP is also available as a stand-alone software package; 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
“euk” eukaryotes
“gram-” Gram-negative prokaryotes
“gram+” Gram-positive prokaryotes

* ‘method’ – prediction method
“nn” neural network only
“hmm” hidden Markov models only
“nn+hmm” both methods (the default)

* ‘sequences’ – protein sequences, with unique identifiers
The sequences 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.
All the input sequences are truncated to 70 aa from the N-terminal.
At most 2,000 sequences and 200,000 amino acids per submission;
each sequence not more than 6,000 amino acids.

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: ‘output’ – prediction results
For each input residue a record is output consisting of the
following fields:

seqname sequence name
source “signalp-3.0-nn” or “signalp-3.0-hmm” (fixed string)
feature “signal” (fixed string)
start,end predicted position of the signal peptide in the
sequence (0-0 is no peptide is predicted)
score prediction score (D score, see the article)
strand,frame N/A
comment answer (“Y” or “S” for yes, “n” or “Q” for no)

CONTACT

Questions concerning the scientific aspects of the SignalP method should go
to Henrik Nielsen, hnielsen@cbs.dtu.dk; technical question concerning the
Web Service should go to Peter Fischer Hallin, pfh@cbs.dtu.dk or Kristoffer
Rapacki, rapacki@cbs.dtu.dk.

Original source
BioCatalogue

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