Service version1_0a_ws0

Contributor URLhttp://www.cbs.dtu.dk/ws/SIDDbase

WSDL URLhttp://www.cbs.dtu.dk/ws/SIDDbase/SIDDbase_1_0a_ws0.wsdl Show/Hide Details

Parser ErrorFailed to access XML Schema component, invalid URL : ws_siddbase_1_0a_ws0.xsd

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

Test #1: SIDDbase test

Retrieves a section of pre-computed SIDD values (synchronous) as well as submitting a small plasmid to calculate SIDD estimates.