Pigeons: A Novel GUI Software for Analysing and Parsing High Density Heterologous Oligonucleotide Microarray Probe...

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• High-density oligonucleotide arrays are used for genomic DNA-based probe selection in heterologous species (Xspecies).
• This approach allows genome and transcriptome studies in non-model or underutilized crop species using microarray platforms.
• A lack of user-friendly software hinders the analysis of probe-level data in cross-species microarray experiments.

Purpose of the Study:

• To develop a novel computer program with a graphical user interface (GUI) for customized array data analysis.
• To enable the analysis of Affymetrix GeneChip probe-level data for cross-species applications.
• To provide tools for probe quality control and species-specific Chip Description File (CDF) generation.

Main Methods:

• Development of the Pigeons software package.
• Utilizing genomic hybridization data to determine empirical boundaries for poor probe removal.
• Implementing visualization and interactive analysis features for datasets.
• Identifying potential Single-Feature Polymorphisms (SFPs) at DNA or RNA levels.

Main Results:

• Pigeons allows users to import and analyze Affymetrix GeneChip probe-level data for Xspecies applications.
• The software facilitates the creation of species-specific CDF files for transcriptomics in heterologous species.
• Pigeons aids in examining experimental designs to detect SFPs.

Conclusions:

• Pigeons provides a valuable GUI-based solution for analyzing cross-species microarray data.
• The software supports customized array data analysis, probe filtering, and SFP identification.
• Pigeons is freely available, promoting its use in genomics and transcriptomics research for understudied species.