shRNA target prediction informed by comprehensive enquiry (SPICE): a supporting system for high-throughput screening of shRNA library

Kenta Kamatuka, Masahira Hattori, Tomoyasu Sugiyama

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

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

Original languageEnglish
Article number7
Pages (from-to)1-9
Number of pages9
JournalEurasip Journal on Bioinformatics and Systems Biology
Volume2016
Issue number1
DOIs
Publication statusPublished - 2016 Dec 1
Externally publishedYes

Fingerprint

High-throughput Screening
RNA Interference
RNA
Small Interfering RNA
Screening
Interference
Throughput
Target
Prediction
Genes
Libraries
Gene
Oligonucleotides
Databases
Reverse Genetics
Spices
Microcomputers
Personal Computer
Sequence Analysis
Web Application

ASJC Scopus subject areas

  • Medicine(all)
  • Computer Science(all)
  • Signal Processing
  • Statistics and Probability
  • General

Cite this

shRNA target prediction informed by comprehensive enquiry (SPICE) : a supporting system for high-throughput screening of shRNA library. / Kamatuka, Kenta; Hattori, Masahira; Sugiyama, Tomoyasu.

In: Eurasip Journal on Bioinformatics and Systems Biology, Vol. 2016, No. 1, 7, 01.12.2016, p. 1-9.

Research output: Contribution to journalArticle

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