An efficient algorithm for systematic analysis of nucleotide strings suitable for siRNA design

BMC Research Notes

Volumn 4, Issue , 2011, Pages

  Baranova, Ancha ^a,b   Bode, Jonathan ^a   Manyam, Ganiraju ^a,c   Emelianenko, Maria ^a  

^a GEORGE MASON UNIVERSITY   (United States)

^b RESEARCH CENTRE FOR MEDICAL GENETICS   (Russian Federation)

^c UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79957449345     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-4-168     Document Type: Article

References (27)

1. Common themes in siRNA-mediated epigenetic silencing pathways. A Verdel A Vavasseur M Le Gorrec L Touat-Todeschini, Int J Dev Biol 2009 53 245 257 10.1387/ijdb.082691av 19412884
2. Gene silencing mediated by small interfering RNAs in mammalian cells. M Scherr MA Morgan M Eder, Curr Med Chem 2003 10 245 256 12570711 (Pubitemid 36131657)
3. Off-targeting and other non-specific effects of RNAi experiments in mammalian cells. P Svoboda, Curr Opin Mol Ther 2007 9 248 257 17608023 (Pubitemid 46944316)
4. Short interfering RNAs can induce unexpected and divergent changes in the levels of untargeted proteins in mammalian cells. PC Scacheri O Rozenblatt-Rosen NJ Caplen TG Wolfsberg L Umayam JC Lee CM Hughes KS Shanmugam A Bhattacharjee M Meyerson FS Collins, Proc Natl Acad Sci USA 2004 101 1892 1897 10.1073/pnas.0308698100 14769924 (Pubitemid 38228987)
5. siRNAs: their potential as therapeutic agents - Part I. Designing of siRNAs. PB Hajeri SK Singh, Drug Discov Today 2009 14 851 858 10.1016/j.drudis.2009.06.001 19540928
6. Guidelines for the selection of highly effective siRNA strings for mammalian and chick RNA interference. K Ui-Tei Y Naito F Takahashi T Haraguchi H Ohki-Hamazaki A Juni R Ueda K Saigo, Nucleic Acids Res 2004 32 936 948 10.1093/nar/gkh247 14769950 (Pubitemid 38854696)
7. A library of siRNA duplexes targeting the phosphoinositide 3-kinase pathway: determinants of gene silencing for use in cell-based screens. AC Hsieh R Bo J Manola F Vazquez O Bare A Khvorova S Scaringe WR Sellers, Nucleic Acids Res 2004 32 893 901 10.1093/nar/gkh238 14769947 (Pubitemid 38854692)
8. A novel siRNA validation system for functional screening and identification of effective RNAi probes in mammalian cells. CF Hung KC Lu TL Cheng RH Wu LY Huang CF Teng WT Chang, Biochem Biophys Res Commun 2006 346 707 720 10.1016/j.bbrc.2006.05.164 16793020
9. Noise amidst the silence: off-target effects of siRNAs? AL Jackson PS Linsley, Trends Genet 2004 20 521 524 10.1016/j.tig.2004.08.006 15475108 (Pubitemid 39314555)
10. Design and validation of siRNAs and shRNAs. F Tilesi P Fradiani V Socci D Willems F Ascenzioni, Curr Opin Mol Ther 2009 11 156 164 19330721
11. OptiRNAi, an RNAi design tool. W Cui J Ning UP Naik MK Duncan, Comput Methods Programs Biomed 2004 75 67 73 10.1016/j.cmpb.2003.09.002 15158049 (Pubitemid 38648879)
12. dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference. Y Naito T Yamada T Matsumiya K Ui-Tei S Morishita, Nucleic Acids Res 2005 33 589 W591 10.1093/nar/gki419 15980542 (Pubitemid 44529990)
13. pssRNAMiner: a plant short small RNA regulatory cascade analysis server. X Dai PX Zhao, Nucleic Acids Res 2008 6 114 11
14. Li W Shum K Truong: 160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA). BMC Bioinformatics 2007 8 185 10.1186/1471-2105-8-185 17555593
15. CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman string alignment. SA Manavski G Valle, BMC Bioinformatics 2008 9 10 19091009
16. siRNA specificity searching incorporating mismatch tolerance data. AM Chalk EL Sonnhammer, Bioinformatics 2008 24 1316 1317 10.1093/bioinformatics/ btn121 18397893 (Pubitemid 351659633)
17. Expression profiling reveals off-target gene regulation by RNAi. AL Jackson SR Bartz J Schelter J Burchard M Mao B Li G Cavet PS Linsley, Nat Biotechnol 2003 21 635 637 10.1038/nbt831 12754523 (Pubitemid 36638089)
18. siRNAs with high specificity to the target: a systematic design by CRM algorithm. T Alsheddi L Vasin R Meduri M Randhawa G Glazko A Baranova, Mol Biol (Mosk) 2008 42 163 171 10.1134/S0026893308010251
19. A comparison of siRNA efficacy predictors. P Saetrom O Snove Jr, Biochem Biophys Res Commun 2004 321 247 253 10.1016/j.bbrc.2004.06.116 15358242 (Pubitemid 39055631)
20. Linear pattern matching algorithm. P Weiner, 14th Annual IEEE Symposium on Switching and Automata Theory 1973 1 11
21. A space-economical suffix tree construction algorithm. EM McCreight, Journal of the ACM 1976 23 262 272 10.1145/321941.321946
22. On-line construction of suffix trees. E Ukkonen, Algorithmica 1995 14 3 249 260 10.1007/BF01206331
23. Truncated suffix trees and their application to data compression. J Na A Apostolico CS Iliopoulos K Park, Theoretical Computer Science 2003 304 87 101 10.1016/S0304-3975(03)00053-7
24. From Ukkonen to McCreight and Weiner: A Unifying View of Linear-Time Suffix Tree Construction. R Giegerich S Kurtz, Algorithmica 1997 19 3 331 353 10.1007/PL00009177 (Pubitemid 127709320)
25. The generalised k-Truncated Suffix Tree for time-and space-efficient searches in multiple DNA or protein sequences. MH Schulz S Bauer PN Robinson, International journal of bioinformatics research and applications 2008 4 81 95 10.1504/IJBRA.2008.017165 18283030 (Pubitemid 351271494)
26. Entropic Profiler - detection of conservation in genomes using information theory. F Fernandes AT Freitas JS Almeida S Vinga, BMC Research Notes 2009 2 72 10.1186/1756-0500-2-72 19416538
27. Fast algorithms for computing sequence distances by exhaustive substring composition. A Apostolico O Denas, Algorithms for Molecular Biology 2008 3 13 10.1186/1748-7188-3-13 18957094