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An Efficient Algorithm for Microarray Probes Re-annotation

  • Pawel Foszner
  • Aleksandra Gruca
  • Andrzej Polanski
  • Michal Marczyk
  • Roman Jaksik
  • Joanna Polanska
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8342)

Abstract

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. However, due to the computational problems related to the whole genome browsing projects, available services and data for re-annotation of microarray probes are still quite sparse. The difficulty in developing systems of re-annotations of microarray probe sets is mainly in huge sizes of probe set data. That’s why we decided to create a effective tool for re-annotation task that will be able to work with such data and could be applied to any species.

In our research we have created an efficient re-annotation method by combining the well known gene search tool BLAT with appropriately designed database. The elaborated system extends possibilities of existing re-annotation tools in the sense that: (1) by tuning parameters of all steps of re-annotation procedure any Affymetrix microarray standard chip can be automatically re-annotated in few hours, (2) several Affymetrix microarray chip standards are already precomputed.

Keywords

re-annotation microarrays expression data affymetrix classification 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Pawel Foszner
    • 1
  • Aleksandra Gruca
    • 1
  • Andrzej Polanski
    • 1
  • Michal Marczyk
    • 1
  • Roman Jaksik
    • 1
  • Joanna Polanska
    • 1
  1. 1.Institute of InformaticsSilesian University of TechnologyGliwicePoland

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