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Method for creating, annotating, and doing a spatial design for a list of gene sequence probes for a gene expression experiment, using a WebService flow

IP.com Disclosure Number: IPCOM000016197D
Original Publication Date: 2002-Nov-23
Included in the Prior Art Database: 2003-Jun-21
Document File: 2 page(s) / 99K

Publishing Venue

IBM

Abstract

This publication describes a method for creating, annotating, and doing a spatial design for a list of gene sequence probes for a gene expression experiment, using a WebService flow This method can be used to automate the probe design and annotation for a set of probes used in a Micro array gene expression experiment using a set of Web Services linked together by a Web Services Work Flow. Currently the researcher in these experiments is required to use a series of application tools, and is expected to manually enter the results from one application as input for the application. This is not only tedious but highly error prone. The procedure described in this disclosure automates the flows of the outputs of one application to the inputs of the applications using Web Services and Web Services Flow Language. The novel approach used in this disclosure defines Web Services for each set of tasks for the Microarray probe design problem, and then suggests definition of a workflow in Web Service Flow Language to initiate the defined Web Services in the correct order. The set of the web services chained together in a web service flow, could automate the selection of probes (sequences) for a micro array experiment.

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  Method for creating, annotating, and doing a spatial design for a list of gene sequence probes for a gene expression experiment, using a WebService flow

    This publication describes a method for creating, annotating, and doing a spatial design for a list of gene sequence probes for a gene expression experiment, using a WebService flow

This method can be used to automate the probe design and annotation for a set of probes used in a Micro array gene expression experiment using a set of Web Services linked together by a Web Services Work Flow.

Currently the researcher in these experiments is required to use a series of application tools, and is expected to manually enter the results from one application as input for the application. This is not only tedious but highly error prone. The procedure described in this disclosure automates the flows of the outputs of one application to the inputs of the applications using Web Services and Web Services Flow Language.

The novel approach used in this disclosure defines Web Services for each set of tasks for the Microarray probe design problem, and then suggests definition of a workflow in Web Service Flow Language to initiate the defined Web Services in the correct order. The set of the web services chained together in a web service flow, could automate the selection of probes (sequences) for a micro array experiment.

Web Services Used

1 Blast -homology

Description: This service will set up filters required for performing the Blast analysis of each of the set of gene sequences with a public/private database. The filters could include a default set of filters.

Inputs: The set of gene sequences from the PubMed Service, the filters for BLAST analysis against public or private databases.

Output: The output from this service would be a set of gene sequences, which would serve as input for other sequence analysis applications.

2 Filtering - GC content, other

Description: The gene sequence chosen for a micro array experiment, should have at least a 50% GC content for it to be a valid probe in the experiment. This service filter...