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SOAP tutorial

You can use MetaGramLocN via SOAP. SOAP enables you to invoke our method from scripts written in your programming language of choice.

MetaLocGramN can be found at BioCatalogue.org!
biocatalog logo

Read more:
http://en.wikipedia.org/wiki/SOAP
Lopez: SOAP-based services provided by the European Bioinformatics Institute NAR 2005

A request description

A SOAP request of MetaGramLocN includes tree functions: predict, get_status, get_result.
 # function gets your sequence,
 # returns a job_id or 'error' if something bad happend ;-(
.predict(seq)

 # !! do not submit sequences shorter than 30 and longer than 3000 !!

 # function gets the job_id given in the predict function
 # returns a state of your request
.get_status(job_id)

 # if your request is done
 # returns a result of the consensus prediction
.get_result(job_id)
WSDL file http://iimcb.genesilico.pl/MetaLocGramN/soap/services.wsdl

Example of a client in Python

You can use whatever library and programing language you want to write your SOAP client script.

In our example, we use Python & SOAP client library SUDS

To install SUDS:
wget https://fedorahosted.org/releases/s/u/suds/python-suds-0.4.tar.gz
tar -zxvf python-suds-0.4.tar.gz 
cd python-suds-0.4/
sudo python setup.py install

You might have to install python-setuptools. However, it is a essential package for many other python packages so it should be in your system already installed.

Then, download the code ...

... and run it!
magnus@maximus:~$ python soap_MetaLocGramN.py 
#job_id: NRODIE
#status: queue
#status: primary prediction::in progress
#status: primary prediction::in progress
#status: primary prediction::done
#status: consenus::done
#status: consenus::done
#status: consenus::done
#status: done
#result: extracellular,47.541,0.0,0.0,0.0,52.459,

primary methods: CELLO,cytoplasmic,0.6138,0.036,0.1346,0.0612,0.1546,
PSLpred,cytoplasmic,0.2,0.531,PSORTb3,unknown,0.2,0.2,0.2,0.2,0.2,
SosuiGramN,cytoplasmic
The result says that your protein has been predicted as a extracellular. Then, there is the list of five (cytoplasm, plasma membrane, periplasm, outer membrane, extracellular) probabilities of belonging the protein to the given localization and the outputs of primary subcellular localization methods.

Below #result line there is the detailed result with the predicted localizations and scores produces by each method.

In summary, the protein is predicted as a extracellular with probabilty 52.459

Enjoy!

If you have any questions, do not hesitate to contact us magnus@genesilico.pl