RNA interference (RNAi) screening is extensively used in the field of reverse genetics. RNAi libraries constructed\nusing random oligonucleotides have made this technology affordable. However, the new methodology requires\nexploration of the RNAi target gene information after screening because the RNAi library includes non-natural\nsequences that are not found in genes. Here, we developed a web-based tool to support RNAi screening. The\nsystem performs short hairpin RNA (shRNA) target prediction that is informed by comprehensive enquiry (SPICE).\nSPICE automates several tasks that are laborious but indispensable to evaluate the shRNAs obtained by RNAi\nscreening. SPICE has four main functions: (i) sequence identification of shRNA in the input sequence (the sequence\nmight be obtained by sequencing clones in the RNAi library), (ii) searching the target genes in the database, (iii)\ndemonstrating biological information obtained from the database, and (iv) preparation of search result files that can\nbe utilized in a local personal computer (PC). Using this system, we demonstrated that genes targeted by random\noligonucleotide-derived shRNAs were not different from those targeted by organism-specific shRNA. The system\nfacilitates RNAi screening, which requires sequence analysis after screening. The SPICE web application is available\nat http://www.spice.sugysun.org/.
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