WSNetCTL_1_1

By | September 22, 2011

INTRODUCTION

This Web Service implements NetCTL v. 1.1. It predicts CTL epitopes
in protein sequences integrating prediction of peptide MHC binding,
proteasomal C terminal cleavage and TAP transport efficiency. The
method is described in detail in the following article:

An integrative approach to CTL epitope prediction. A combined
algorithm integrating MHC-I binding, TAP transport efficiency,
and proteasomal cleavage predictions.
Larsen MV, Lundegaard C, Kasper Lamberth, Buus S. Brunak S,
Lund O, and Nielsen M.
European Journal of Immunology 35(8): 2295-303, 2005

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

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

NetCTL is also available as a stand-alone software package; write to
software@cbs.dtu.dk for details.
NetCTL 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?netCTL

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:

* ‘supertype’ – HLA supertype
10 HLA supertypes are available:
A1, A2, A3, A24, B7, B8, B27, B44, B58 and B62;

* ‘wcle’ – weight on C terminal cleavage
The value 0.1 gives optimal predictive performance on the average.

* ‘wtap’ – weight on TAP transport efficiency
The value 0.05 gives optimal predictive performance on the average.

* ‘threshold’ – threshold for epitope identification
Peptides with a combined prediction score value greater than the
threshold value are marked as potential epitopes. In a large scale
benchmark identifying known CTL epitope in proteins the default
value of 0.75 was found to correspond to a sensitivity of 0.65
and a specificity 0.97. Note that the benchmark is highly
unbalanced since only one peptide is identified as CTL epitope
in each protein, and the number of negatives hence is orders of
magnitude larger than the number of positives. This has important
implications for the interpretation of the specificity values.

* ‘sort’ – output sorting on score
Possible values are 0 (sorting on the combined score), 1 (MHC),
2 (Cle), 3 (TAP) and negative (no sorting)

* ‘sequences’ – protein sequences, with unique identifiers
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: ‘output’ – prediction results
For each input residue a record is output consisting of the
following fields:

seqname truncated to 12 characters in ver. 1.1a
source “netCTL-1.1″ (fixed string)
feature “CTL” (fixed string)
start,end residue number (given twice)
score prediction score (combined)
strand,frame N/A
comment Text string consisting of:

* Predicted MHC binding affinity
The value is give as 1 – log50k(aff), where log50k
is the logaritm with base 50.000, and aff is the
affinity in nM units;
* Rescaled binding affinity
The predicted binding affinity is normalized by the
1% fractil
* C terminal cleavage affinity
* TAP transport efficiency

“-E” to indicate the identified MHC ligands (when
the combined score is greater than the threshold).

CONTACT

Questions concerning the scientific aspects of the NetCTL method should go
to Morten Nielsen, mniel@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
WSNetCTL_1_1
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 NetCTL v. 1.1. It predicts CTL epitopes in protein sequences integrating prediction of peptide MHC [...]

Further information

INTRODUCTION

This Web Service implements NetCTL v. 1.1. It predicts CTL epitopes
in protein sequences integrating prediction of peptide MHC binding,
proteasomal C terminal cleavage and TAP transport efficiency. The
method is described in detail in the following article:

An integrative approach to CTL epitope prediction. A combined
algorithm integrating MHC-I binding, TAP transport efficiency,
and proteasomal cleavage predictions.
Larsen MV, Lundegaard C, Kasper Lamberth, Buus S. Brunak S,
Lund O, and Nielsen M.
European Journal of Immunology 35(8): 2295-303, 2005

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

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

NetCTL is also available as a stand-alone software package; write to
software@cbs.dtu.dk for details.
NetCTL 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?netCTL

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:

* ‘supertype’ – HLA supertype
10 HLA supertypes are available:
A1, A2, A3, A24, B7, B8, B27, B44, B58 and B62;

* ‘wcle’ – weight on C terminal cleavage
The value 0.1 gives optimal predictive performance on the average.

* ‘wtap’ – weight on TAP transport efficiency
The value 0.05 gives optimal predictive performance on the average.

* ‘threshold’ – threshold for epitope identification
Peptides with a combined prediction score value greater than the
threshold value are marked as potential epitopes. In a large scale
benchmark identifying known CTL epitope in proteins the default
value of 0.75 was found to correspond to a sensitivity of 0.65
and a specificity 0.97. Note that the benchmark is highly
unbalanced since only one peptide is identified as CTL epitope
in each protein, and the number of negatives hence is orders of
magnitude larger than the number of positives. This has important
implications for the interpretation of the specificity values.

* ‘sort’ – output sorting on score
Possible values are 0 (sorting on the combined score), 1 (MHC),
2 (Cle), 3 (TAP) and negative (no sorting)

* ‘sequences’ – protein sequences, with unique identifiers
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: ‘output’ – prediction results
For each input residue a record is output consisting of the
following fields:

seqname truncated to 12 characters in ver. 1.1a
source “netCTL-1.1″ (fixed string)
feature “CTL” (fixed string)
start,end residue number (given twice)
score prediction score (combined)
strand,frame N/A
comment Text string consisting of:

* Predicted MHC binding affinity
The value is give as 1 – log50k(aff), where log50k
is the logaritm with base 50.000, and aff is the
affinity in nM units;
* Rescaled binding affinity
The predicted binding affinity is normalized by the
1% fractil
* C terminal cleavage affinity
* TAP transport efficiency

“-E” to indicate the identified MHC ligands (when
the combined score is greater than the threshold).

CONTACT

Questions concerning the scientific aspects of the NetCTL method should go
to Morten Nielsen, mniel@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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