MiRPara: A SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Wu, Yonggan ^a,b   Wei, Bo ^a   Liu, Haizhou ^a   Li, Tianxian ^a   Rayner, Simon ^a  

^a WUHAN INSTITUTE OF VIROLOGY   (China)

^b TEXAS TECH UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CODING REGION; EFFECTIVE TOOL; GENOME SEQUENCES; IDENTIFICATION METHOD; POST-TRANSCRIPTIONAL; REGULATORY PROCESS; SMALL DATA SET; SPECIES SPECIFICS;

COMPUTER SOFTWARE; FORECASTING; GENES; IDENTIFICATION (CONTROL SYSTEMS); SUPPORT VECTOR MACHINES; TRANSCRIPTION;

RNA;

ANIMALIA;

MICRORNA;

ANIMAL; ARTICLE; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; CONFORMATION; GENETICS; GENOME; HUMAN; METABOLISM; METHODOLOGY; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; SPECIES DIFFERENCE;

ANIMALS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; GENOME; HUMANS; MICRORNAS; NUCLEIC ACID CONFORMATION; OPEN READING FRAMES; SOFTWARE; SPECIES SPECIFICITY;

EID: 79958033251     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-107     Document Type: Article

References (44)

1. He L, Hannon GJ. MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 2004, 5(7):522-531. 10.1038/nrg1379, 15211354.
2. Pfeffer S, Zavolan M, Grasser FA, Chien M, Russo JJ, Ju J, John B, Enright AJ, Marks D, Sander C, et al. Identification of virus-encoded microRNAs. Science 2004, 304(5671):734-736. 10.1126/science.1096781, 15118162.
3. Brennecke J, Hipfner DR, Stark A, Russell RB, Cohen SM. bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 2003, 113(1):25-36. 10.1016/S0092-8674(03)00231-9, 12679032.
4. Xu P, Vernooy SY, Guo M, Hay BA. The Drosophila microRNA Mir-14 suppresses cell death and is required for normal fat metabolism. Curr Biol 2003, 13(9):790-795. 10.1016/S0960-9822(03)00250-1, 12725740.
5. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 2006, (34 Database):D140-144.
6. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, (36 Database):D154-158.
7. Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B, Cooch N, Shiekhattar R. The Microprocessor complex mediates the genesis of microRNAs. Nature 2004, 432(7014):235-240. 10.1038/nature03120, 15531877.
8. Zeng Y, Cullen BR. Recognition and cleavage of primary microRNA transcripts. Methods Mol Biol 2006, 342:49-56.
9. Yi R, Qin Y, Macara IG, Cullen BR. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev 2003, 17(24):3011-3016. 10.1101/gad.1158803, 305252, 14681208.
10. Tijsterman M, Plasterk RH. Dicers at RISC; the mechanism of RNAi. Cell 2004, 117(1):1-3.
11. Lee YS, Nakahara K, Pham JW, Kim K, He Z, Sontheimer EJ, Carthew RW. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 2004, 117(1):69-81. 10.1016/S0092-8674(04)00261-2, 15066283.
12. Lin SL, Chang D, Ying SY. Asymmetry of intronic pre-miRNA structures in functional RISC assembly. Gene 2005, 356:32-38. 1788082, 16005165.
13. Rand TA, Ginalski K, Grishin NV, Wang X. Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activity. Proc Natl Acad Sci USA 2004, 101(40):14385-14389. 10.1073/pnas.0405913101, 521941, 15452342.
14. Szittya G, Moxon S, Santos DM, Jing R, Fevereiro MP, Moulton V, Dalmay T. High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genomics 2008, 9:593. 10.1186/1471-2164-9-593, 2621214, 19068109.
15. Burnside J, Ouyang M, Anderson A, Bernberg E, Lu C, Meyers BC, Green PJ, Markis M, Isaacs G, Huang E, et al. Deep sequencing of chicken microRNAs. BMC Genomics 2008, 9:185. 10.1186/1471-2164-9-185, 2375912, 18430245.
16. Skalsky RL, Cullen BR. Viruses, microRNAs, and host interactions. Annu Rev Microbiol 2010, 64:123-141. 10.1146/annurev.micro.112408.134243, 20477536.
17. Wang X, Zhang J, Li F, Gu J, He T, Zhang X, Li Y. MicroRNA identification based on sequence and structure alignment. Bioinformatics 2005, 21(18):3610-3614. 10.1093/bioinformatics/bti562, 15994192.
18. Hertel J, Stadler PF. Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data. Bioinformatics 2006, 22(14):e197-202. 10.1093/bioinformatics/btl257, 16873472.
19. Brameier M, Wiuf C. Ab initio identification of human microRNAs based on structure motifs. BMC Bioinformatics 2007, 8:478. 10.1186/1471-2105-8-478, 2238772, 18088431.
20. Lai EC, Tomancak P, Williams RW, Rubin GM. Computational identification of Drosophila microRNA genes. Genome Biol 2003, 4(7):R42. 10.1186/gb-2003-4-7-r42, 193629, 12844358.
21. Jones-Rhoades MW, Bartel DP. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 2004, 14(6):787-799. 10.1016/j.molcel.2004.05.027, 15200956.
22. Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB, Bartel DP. The microRNAs of Caenorhabditis elegans. Genes Dev 2003, 17(8):991-1008. 10.1101/gad.1074403, 196042, 12672692.
23. Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A, Einat P, Einav U, Meiri E, et al. Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet 2005, 37(7):766-770. 10.1038/ng1590, 15965474.
24. Huang TH, Fan B, Rothschild MF, Hu ZL, Li K, Zhao SH. MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans. BMC Bioinformatics 2007, 8:341. 10.1186/1471-2105-8-341, 2206061, 17868480.
25. Ritchie W, Theodule FX, Gautheret D. Mireval: a web tool for simple microRNA prediction in genome sequences. Bioinformatics 2008, 24(11):1394-1396. 10.1093/bioinformatics/btn137, 18453555.
26. Artzi S, Kiezun A, Shomron N. miRNAminer: a tool for homologous microRNA gene search. BMC Bioinformatics 2008, 9:39. 10.1186/1471-2105-9-39, 2258288, 18215311.
27. Xu Y, Zhou X, Zhang W. MicroRNA prediction with a novel ranking algorithm based on random walks. Bioinformatics 2008, 24(13):i50-58. 10.1093/bioinformatics/btn175, 2718653, 18586744.
28. Yousef M, Nebozhyn M, Shatkay H, Kanterakis S, Showe LC, Showe MK. Combining multi-species genomic data for microRNA identification using a Naive Bayes classifier. Bioinformatics 2006, 22(11):1325-1334. 10.1093/bioinformatics/btl094, 16543277.
29. Helvik SA, Snove O, Saetrom P. Reliable prediction of Drosha processing sites improves microRNA gene prediction. Bioinformatics 2007, 23(2):142-149. 10.1093/bioinformatics/btl570, 17105718.
30. Moissiard G, Voinnet O. RNA silencing of host transcripts by cauliflower mosaic virus requires coordinated action of the four Arabidopsis Dicer-like proteins. Proc Natl Acad Sci USA 2006, 103(51):19593-19598. 10.1073/pnas.0604627103, 1698440, 17164336.
31. Chapman EJ, Carrington JC. Specialization and evolution of endogenous small RNA pathways. Nat Rev Genet 2007, 8(11):884-896. 10.1038/nrg2179, 17943195.
32. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003, 31(13):3406-3415. 10.1093/nar/gkg595, 169194, 12824337.
33. Mathews DH, Sabina J, Zuker M, Turner DH. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 1999, 288(5):911-940. 10.1006/jmbi.1999.2700, 10329189.
34. Han J, Lee Y, Yeom KH, Nam JW, Heo I, Rhee JK, Sohn SY, Cho Y, Zhang BT, Kim VN. Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 2006, 125(5):887-901. 10.1016/j.cell.2006.03.043, 16751099.
35. Chen PH, Fan RE, Lin CJ. A study on SMO-type decomposition methods for support vector machines. IEEE Trans Neural Netw 2006, 17(4):893-908. 10.1109/TNN.2006.875973, 16856653.
36. Chang CC, Hsu CW, Lin CJ. The analysis of decomposition methods for support vector machines. IEEE Trans Neural Netw 2000, 11(4):1003-1008. 10.1109/72.857780, 18249827.
37. Chan PP, Lowe TM. GtRNAdb: a DATABASE of transfer RNA genes detected in genomic sequence. Nucleic Acids Res 2009, (37 Database):D93-97.
38. Allen E, Xie Z, Gustafson AM, Carrington JC. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 2005, 121(2):207-221. 10.1016/j.cell.2005.04.004, 15851028.
39. Appasani K, . (ed) MicroRNAs: from basic science to disease biology. 2007, Cambridge University Press, (ed).
40. Vermeulen A, Behlen L, Reynolds A, Wolfson A, Marshall WS, Karpilow J, Khvorova A. The contributions of dsRNA structure to Dicer specificity and efficiency. RNA 2005, 11(5):674-682. 10.1261/rna.7272305, 1370754, 15811921.
41. Elbashir SM, Martinez J, Patkaniowska A, Lendeckel W, Tuschl T. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J 2001, 20(23):6877-6888. 10.1093/emboj/20.23.6877, 125328, 11726523.
42. Parker JS, Roe SM, Barford D. Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. EMBO J 2004, 23(24):4727-4737. 10.1038/sj.emboj.7600488, 535097, 15565169.
43. Ng Kwang Loong S, Mishra SK. Unique folding of precursor microRNAs: quantitative evidence and implications for de novo identification. RNA 2007, 13(2):170-187. 1781370, 17194722.
44. Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 2006, 127(6):1193-1207. 10.1016/j.cell.2006.10.040, 17174894.