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Open Access Highly Accessed Methodology article

An efficient RNA interference screening strategy for gene functional analysis

Chih-Hung Chang1, Hsiang-Iu Wang1, Hsiang-Chia Lu2, Cheng-En Chen2, Hong-Hwa Chen345, Hsin-Hung Yeh26* and Chuan Yi Tang17*

Author Affiliations

1 Department of Computer Science, National Tsing Hua University, Hsinchu, 30013, Taiwan

2 Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, 10617, Taiwan

3 Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan

4 Orchid Research Center, National Cheng Kung University, Tainan, 701, Taiwan

5 Institute of Tropical Plant Scicenes, National Cheng Kung University, Tainan, 701, Taiwan

6 Research Center for Plant Medicine, National Taiwan University, Taipei, 10617, Taiwan

7 Department of Computer Science and Information Engineering, Providence University, Taichung, 43301, Taiwan

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BMC Genomics 2012, 13:491  doi:10.1186/1471-2164-13-491

Published: 18 September 2012

Additional files

Additional file 1:

Figures S1 and S2. A simple example of a powerful subsequence P, and the dotplot of TF15 and TF21 sequences.

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Open Data

Additional file 2:

Proof to prove that the problem of finding a qualified sequence r maximizing the size of T is NP-complete.

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Additional file 3:

Methods the detail of our modified greedy algorithm for selecting qualified siRNAs to perform the first-round RNAi analysis.

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Additional file 4:

Tables S1-3. The lists of the siRNAs that were selected for first-round RNAi analysis with different parameters.

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