IMAD: flexible annotation of microarray sequences

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IMAD: flexible annotation of microarray sequences

BACKGROUND Accurate and current functional annotation of microarray probes is essential for the analysis and interpretation of the biological processes involved. As gene structures and functional annotation are updated in genome databases, the annotation attached to microarray probes must be updated so that scientists have access to the latest information with which to analyse their data. RES...

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Re-Annotator: Annotation Pipeline for Microarray Probe Sequences

Microarray technologies are established approaches for high throughput gene expression, methylation and genotyping analysis. An accurate mapping of the array probes is essential to generate reliable biological findings. However, manufacturers of the microarray platforms typically provide incomplete and outdated annotation tables, which often rely on older genome and transcriptome versions that ...

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Annotation of the Affymetrix porcine genome microarray.

Overview: The Affymetrix porcine genome microarray (http:// www.affymetrix.com/products/arrays/specific/porcine.affx) is minimally annotated. Less than 10% of the probe sets on this array are described with gene names, posing a challenge to biological interpretation of data. Lack of annotation is likely due to the limited availability of full-length porcine cDNA sequence. Presented here is a st...

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Efficient Algorithm for Microarray Probes Re-annotation

Systems for re-annotations of DNA microarray data for supporting analysis of results of DNA microarray experiments are becoming important elements of bioinformatics aspects of gene expression based studies [10]. However, due to the computational problems related to the whole genome browsing projects, available services and data for reannotation of microarray probes are still quite sparse. The d...

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GandrKB--ontological microarray annotation and visualization

SUMMARY The Gandr (gene annotation data representation) knowledgebase is an ontological framework for laboratory-specific gene annotation. Gandr uses Protege 2000 for editing, querying and visualizing microarray data and annotations. Genes can be annotated with provided, newly created or imported ontological concepts. Annotated genes can inherit assigned concept properties and can be related to...

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ژورنال

عنوان ژورنال: BMC Proceedings

سال: 2009

ISSN: 1753-6561

DOI: 10.1186/1753-6561-3-s4-s2