MkDom2

1899

Service version1.0

Contributor URLhttp://prodom.prabi.fr/prodom/current/documentation/mkdom2.html

WSDL URLhttp://prodom.prabi.fr/prodom/current/wsdl/essairunmkdom.wsdl PASSED

MkDom2 is the program used routinely to build each new release of ProDom. The algorithm relies on the assumption that the shortest amino acid sequence corresponds to a single domain, and may be used as a query to screen the database with the psi-blast program, in order to cluster homologous domains. To build ProDom, we run this program on the UniProt (swissprot/trembl) Knowledge Database, but it can be run on any set of protein sequences in a fasta file.

Inputs:

a file containing the sequences to analyse in fasta format
psi-blast parameters. Default will be -j 10 -e 0.01 -h 0.01. If you want to change something please enter INTER= value to change -j option, E_EXPECT=value for -e option and H_EXPECT=value for -h option.

Outputs:

the log file

the alignment file of the sequences in srs format

the results of the analysis in xdom format

the project file used to launch xdom faster

A perl script is available here to run this webservice from your computer. Please install SOAP Lite before.

A description of the WSDL service:

MkDomService

Namespace: http://prodom.prabi.fr/mkdom

Port: MkDomPort
Location: http://prodom.prabi.fr/prodom/2006.1/cgi-bin/essaimkdom.cgi
Protocol: http://schemas.xmlsoap.org/soap/http
Default Style: document

Operations

runMkDom

Calculate mkdom on fasta data

SOAP Action: http://prodom.prabi.fr/mkdom#runMkDom
Input Message: MkDomRequestMsg
- inputWrapper
  - runMkDom type
    - InputFastaSeqs type string
    - ParametersBlast type string
Output Message: MkDomResponseMsg
- outputWrapper
  - runMkDomResponse type
    - output_in_mkdom_format type string
    - log_output type string
    - alignment_output type string
    - project_file type string

WSDL Changes

Date	Description of Changes
3rd June 2009	First Snapshot

Test #1: mkdomTest

This is a test for the MkDom2 webservice. It uses perl and SOAPlite. It includes a test using a short fasta file (7 sequences) as input and checks whether :

the output is not empty
the first output element is in correct xdom format and contains 7 elements
the second output element (the log file) indicates a normal end of the program
the third output element is in correct srs format and contains 4 domain families
the last output element is a valid url to webdom (domain visualization)

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".....MkDom2 is the program used routinely to build each new release of ProDom. The algorithm relies on the assumption that the shortest amino acid sequence corresponds to a single domain, and may be used as a query to screen the database with the psi-blast program, in order to cluster homologous domains. To build ProDom, we run this program on the UniProt (swissprot/trembl) Knowledge Database, but it can be run on any set of protein sequences in a fasta file......"

This program is amazing and the people behind this wonderful project is awesome, but I was wondering How this algorithm work, I mean Can the author of this, can post here further explanation about this program. TIA

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Submitted by blue_rose on Mon, 01/25/2010 - 18:52.

This program can be run on the UniProt (swissprot/trembl) Knowledge Database, but it can be run on any set of protein sequences in a fasta file. Prodom is really a good tool many of my colleagues have tried it and it works good.
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