CEM-Designer: design of custom expression microarrays in the post-ENCODE era

Microarrays are widely used in gene expression studies, and custom expression microarrays are popularto monitor expression changes of a customer-defined set of genes. However, the complexity of transcriptomesuncovered recently make custom expression microarray design a non-trivial task. Pervasivetranscription and alternative processing of transcripts generate a wealth of interweaved transcripts thatrequires well-considered probe design strategies and is largely neglected in existing approaches.We developed the web server CEM-Designer that facilitates microarray platform independent designof custom expression microarrays for complex transcriptomes. CEM-Designer covers (i) the collectionand generation of a set of unique target sequences from different sources and (ii) the selection of a set ofsensitive and specific probes that optimally represents the target sequences. Probe design itself is left tothird party software to ensure that probes meet provider-specific constraints.CEM-Designer is available at http://designpipeline.bioinf.uni-leipzig.de.