Web Service SIDDbase SOAP Dk

Cog_error Archived / Deprecated

This service has been archived because it may not be active anymore (or is close to being non active). Please do not use it as it may not be accessible.

Specified Name (from WSDL): WSSIDDbase_1_0 |
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Annotations: 14 Total number of annotations from the provider's definition / description document. 1 Total number of annotations submitted by members of BioCatalogue. 9 Total number of annotations sourced from other registries. 4

Overview

Provider:
Center for Biological Sequence Analysis (CBS)

Location:
Denmark Dk

Submitter/Source:
Franck TanohGb (over 11 years ago)

Base URL:
http://ws.cbs.dtu.dk/cgi-bin/soap/ws/simple.cgi

WSDL Location:
http://www.cbs.dtu.dk/ws/SIDDbase/SIDDbase_1_0.wsdl (download last cached WSDL file)

Description(s):
from provider's description doc (over 11 years ago)

SIDDbase-WS is a SOAP based Web Service created in a collaboration between the Comparative Microbial Genomics Group at CBS, The Technical University of Denmark and Prof. Craig Benham’s research group at the UC Davis Genome Center. It provides interoperable access to the SIDD software, and access to the repository of stored results from calculations previously performed on complete bacterial genomes.

SIDD (Stress-induced DNA Duplex Destabilization) is the propensity for the DNA duplex to be destabilized within genomic regions that are experiencing a superhelical stress. This is a complex, interactive attribute of genomic DNA, that has been implicated in a wide variety of regulatory processes. Different strategies are used to calculate SIDD properties of short (i.e. < ~10kb) regions (Bi C, Benham CJ., WebSIDD: A server for predicting stress-induced duplex destabilized (SIDD) sites in superhelical DNA, Bioinformatics, 2004 Jun 12;20(9):1477-9), and of long genomic sequences, up to complete chromosomes (Benham CJ and Bi C, The Analysis of Stress-Induced Duplex Destabilization in Long Genomic DNA Sequences, J. Comp. Biol. 11: 519-543, 2004). The extent of destabilization is given by sigma, the superhelix density. For each base pair and each sigma value two results are reported. These are the probability p(x) of base pair x being open (i.e. separated) under the given conditions, and the increment G(x) of free energy needed to insure that base pair x is always open then.

This service consist of two parts:

  1. REPOSITORY A repository of pre-calculated SIDD values (for four different sigma values -0.025, -0.035,-0.045,-0.055,-0.065). This repository is updated daily by synchronizing prokaryotic genome sequences against NCBI Entrez Genome Projects (http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi). Any new or changed genomes will be updated automatically every day. The DNA geometry (i.e., whether the chromosome is circular or linear) is by default circular, which will be used except in the cases where the GenBank record indicates a linear chromosome. This part of the service runs synchronously, which means that the user will receive the output directly as a response to a request message

  2. CALCULATION SERVICE An SOAP compliant interface for making SIDD predictions. This part of the service runs /a/synchronously, and is therefore split into three different operations submit, poll, and fetch operations

REPOSITORY
1. getSIDD
	Get the genomic sequence by specifying the GenBank accession number
	Input: 
				* 'accession'    - The Genbank accession number (e.g. AL111168) 
				                   of the genome sequence you want to fetch from the
				                   repository.
				* 'sigma'        - The sigma value of the prediction (-0.025,-0.035,-0.045,-0.055,-0.065)
				* 'energetics'   - Energetics used in the calculations. Only copolymeric is supported
				                   by the repository (c)
				* 'weight'       - The overlap/weighting scheme. Only 10 is supported by the repository (10)
				* 'from'         - (optional) From (and including this) postion 
				* 'to'           - (optional) To (and including this) postion
				* 'Gformat'      - e.g. '%.2f'
				* 'Pformat'      - e.g. '%.2e'
				* 'format'       - Either 'string' or 'element' - determins if output should be 
				                   provided as XML entities are comma separated strings. The latter
				                   is much faster.
	Output:
				* 'accession'    - The ganbank accession of the record used.
				* 'digest'       - The MD5 checksum of the entire genomic DNA sequence.
				* 'from'         - From (and including this) postion.
				* 'to'           - To (and including this) postion.
				* 'total_length' - Total length of genome sequence.
				* 'version'      - SIDD back-end program version. 
				* 'method'       - The energetics method used.
				* 'weight'       - The overlap/weighting scheme.
				* 'sigma'        - The sigma value of the prediction.

         The following two elements consists of a choice (depending on 
         'format' specified in request)
				* 'element'      
				 *  'x'          - Absolute chromosomal position
				 *  'nt'         - The nucleotide at position 'x'
				 *  'P'          - The helix opening probability.
				 *  'G'          - Free energy, G.
				* 'string'      
				 *  'P'          - Comma separated list of probabilities
				 *  'G'          - Comma separated list of free energies


CALCULATION
2a. runService
	Submit a custom DNA sequnce to the SIDD program
	Input:
				* 'sequencedata'
				 * 'sequence'
					* 'seq'        - The raw DNA sequence
					* 'id'         - Any sequence identifier
				* 'sigma'        - The sigma value of the prediction (e.g. -0.055)
				* 'energetics'   - Either copolymeric (c) or nearest-neighbor energetics (n)
				* 'weight'       - The overlap/weighting scheme. Only 10 is supported by the repository (10)
				* 'Gformat'      - e.g. '%.2f'
				* 'Pformat'      - e.g. '%.2e'
      * 'format'       - Either 'string' or 'element' - determins if output should be 
				                   provided as XML entities are comma separated strings. The latter
				                   is much faster.		
	Output:
				* 'jobid'        - The 32 byte identification string of the job
				* 'datetime'     - The last timepoint at which the status of the job has changed
				* 'status'       - Possible values are QUEUED, ACTIVE, FINISHED, WAITING, REJECTED, 
				                   UNKNOWN JOBID or QUEUE DOWN

2b. pollQueue
Once obtained from 'runService', a job identification can be used to poll the
status to see if the result is ready for download.

	Input:
				* 'jobid'        - The 32 byte identification string of the job
	Output:
				* 'jobid'        - The 32 byte identification string of the job
				* 'datetime'     - The last timepoint at which the status of the job has changed
				* 'status'       - Possible values are QUEUED, ACTIVE, FINISHED, WAITING, REJECTED, 
				                   UNKNOWN JOBID or QUEUE DOWN

2c. fetchResult
Once the status is 'FINISHED' the results generated by the Web Service can be retrieved by
specifying the jobid;

	Input:  
				* 'jobid'        - The 32 byte identification string of the job
	Output:
				* 'total_length' - Total length of genome sequence.
				* 'version'      - SIDD back-end program version. 
				* 'method'       - The energetics method used.
				* 'weight'       - The overlap/weighting scheme.
				* 'sigma'        - The sigma value of the prediction.

         The following two elements consists of a choice (depending on 
         'format' specified in request)
				* 'element'      
				 *  'x'          - Absolute chromosomal position
				 *  'nt'         - The nucleotide at position 'x'
				 *  'P'          - The helix opening probability.
				 *  'G'          - Free energy, G.
				* 'string'      
				 *  'P'          - Comma separated list of probabilities
				 *  'G'          - Comma separated list of free energies

	For more information, please contact Peter F. Hallin: pfh@cbs.dtu.dk
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