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Pigeons: a novel GUI software for analysing and parsing high density heterologous oligonucleotide microarray probe level data

Lai, Hung-Ming; May, Sean; Mayes, Sean

Pigeons: a novel GUI software for analysing and parsing high density heterologous oligonucleotide microarray probe level data Thumbnail


Authors

Hung-Ming Lai

SEAN MAYES SEAN.MAYES@NOTTINGHAM.AC.UK
Associate Professor



Abstract

Genomic DNA-based probe selection by using high density oligonucleotide arrays has recently been applied to heterologous species (Xspecies). With the advent of this new approach, researchers are able to study the genome and transcriptome of a non-model or an underutilised crop species through current state-of-the-art microarray platforms. However, a software package with a graphical user interface (GUI) to analyse and parse the oligonucleotide probe pair level data is still lacking when an experiment is designed on the basis of this cross species approach. A novel computer program called Pigeons has been developed for customised array data analysis to allow the user to import and analyse Affymetrix GeneChip® probe level data through XSpecies. One can determine empirical boundaries for removing poor probes based on genomic hybridisation of the test species to the Xspecies array, followed by making a species-specific Chip Description File (CDF) file for transcriptomics in the heterologous species, or Pigeons can be used to examine an experimental design to identify potential Single-Feature Polymorphisms (SFPs) at the DNA or RNA level. Pigeons is also focused around visualization and interactive analysis of the datasets. The software with its manual (the current release number version 1.2.1) is freely available at the website of the Nottingham Arabidopsis Stock Centre (NASC).

Journal Article Type Article
Publication Date Jan 1, 2014
Deposit Date Apr 29, 2014
Publicly Available Date Apr 29, 2014
Journal Microarrays
Electronic ISSN 2076-3905
Publisher MDPI
Peer Reviewed Peer Reviewed
Volume 3
Issue 1
DOI https://doi.org/10.3390/microarrays3010001
Public URL https://nottingham-repository.worktribe.com/output/997482
Publisher URL http://www.mdpi.com/2076-3905/3/1/1

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