Annotation and specificity of existing genome-wide small interfering RNA libraries

Large-scale RNA interference experiments, especially the ones based on short-interfering RNA (siRNA) technology have become increasingly popular over the past years. Obviously, the sequence (and structure) of the corresponding siRNA is a key factor in obtaining reliable results in these large-scale studies, and the companies use a variety of algorithms to design them. Design tools have been developed based on experimental data to increase the knockdown efficiency of siRNAs. Nevertheless, as the genome annotations are still continuously changing, siRNAs may become obsolete, so siRNA reagents should be periodically re-annotated according the latest version of sequence database. In this article, existing siRNA design algorithms, design parameters, and siRNAs are evaluated. A new approach for systematic analysis and re-annotation of siRNAs libraries produced in the last decade is introduced here.