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Generation of Two-color Antigen Microarrays for the Simultaneous Detection of IgG and IgM Autoantibodies

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Published on: September 15, 2016

A Java-based tool for the design of classification microarrays.

Da Meng¹, Shira L Broschat, Douglas R Call

¹School of Electrical Engineering and Computer Science, Washington State University, Pullman, USA. dmeng@eecs.wsu.edu

BMC Bioinformatics

|August 6, 2008

Summary

This summary is machine-generated.

We developed PLASMID, a Java tool for selecting optimal probe sets for mixed microarrays used in bacterial classification and genetic analysis. This software minimizes redundancy and enhances diversity representation for more effective microbial identification.

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Area of Science:

Bioinformatics
Microbiology
Genomics

Background:

Classification microarrays are crucial for bacterial strain identification and epidemiological studies.
Mixed microarrays, containing DNA from multiple organisms, offer greater effectiveness than single-organism arrays.
Optimizing probe selection is vital to prevent redundancy and ensure comprehensive diversity representation in microarrays.

Purpose of the Study:

To introduce PLASMID, a Java-based software tool designed for selecting minimal probe sets for classification microarrays.
To address the challenges of probe redundancy and limited diversity representation in mixed microarray design.
To provide a versatile tool applicable to both mixed-plasmid and expression microarray design.

Main Methods:

PLASMID utilizes a novel approach for probe redundancy reduction.
Probe selection is achieved through stepwise discriminant analysis.
The software incorporates various clustering, ranking, and display methods, supporting multiple data input formats.

Main Results:

PLASMID was successfully applied to diverse datasets, including existing mixed-plasmid microarray data.
Its utility was demonstrated with a virtual mixed-genome microarray of *Streptococcus* strains.
Application to expression microarray data confirmed the software's broad applicability.

Conclusions:

PLASMID is a new software tool for selecting probe sets for classification microarrays, particularly effective for mixed-plasmid designs.
The tool's flexibility extends to designing expression arrays, offering user-selectable analysis and display options.
PLASMID can construct virtual microarrays for identifying optimal probe sets and supports data storage for subsequent analyses.