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 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. 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.