Detecting miRNAs in deep-sequencing data: A software performance comparison and evaluation

Briefings in Bioinformatics

Volumn 14, Issue 1, 2013, Pages 36-45

  Williamson, Vernell ^a   Kim, Albert ^a   Xie, Bin ^b   Omari McMichael, G ^c   Gao, Yuan ^b   Vladimirov, Vladimir ^d  

^a VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

^b LIEBER INSTITUTE FOR BRAIN DEVELOPMENT   (United States)

^c Virginia Institute of Psychiatric and Behavioral Genetics   (United States)

^d VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

Author keywords

Comparison; Deep sequencing; miRNA detection; Software

Indexed keywords

MICRORNA;

ALGORITHM; ANIMAL; ARTICLE; BIOLOGY; COMPARATIVE STUDY; COMPUTER PROGRAM; EVALUATION; GENETICS; HUMAN; NUCLEIC ACID DATABASE; SEQUENCE ANALYSIS; STATISTICS; TUMOR CELL LINE; VALIDATION STUDY;

ALGORITHMS; ANIMALS; CELL LINE, TUMOR; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; HUMANS; MICRORNAS; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 84872797404     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbs010     Document Type: Article

References (36)

1. Krol J, Krzyzosiak WJ. Structural aspects of microRNA biogenesis. IUBMB Life 2004;56:95-100.
2. Li Y, Lin L, Jin P. The microRNA pathway and fragile X mental retardation protein. Biochim Biophys Acta 2008;1779: 702-5.
3. Mencia A, Modamio-Hoybjor S, Redshaw N, et al. Mutations in the seed region of human miR-96 are responsible for nonsyndromic progressive hearing loss. Nat Genet 2009;41:609-13.
4. Scalbert E, Bril A. Implication of microRNAs in the cardiovascular system. Curr Opin Pharmacol 2008;8:181-8.
5. Oulas A, Boutla A, Gkirtzou K, et al. Prediction of novel microRNA genes in cancer-associated genomic regions-a combined computational and experimental approach. Nucleic Acids Res 2009;37:3276-87.
6. Saetrom P, Snove O, Nedland M, et al. Conserved MicroRNA characteristics in mammals. Oligonucleotides 2006;16:115-44.
7. Kim VN. MicroRNA biogenesis: coordinated cropping and dicing. Nat RevMol Cell Biol 2005;6:376-85.
8. Kim YK, Kim VN. Processing of intronic microRNAs. EMBOJ 2007;26:775-83.
9. Rodriguez A, Griffiths-Jones S, Ashurst JL, et al. Identification of mammalian microRNA host genes and transcription units. Genome Res 2004;14:1902-10.
10. Erdmann VA, Szymanski M, Hochberg A, Groot N, Barciszewski J. Non-coding, mRNA-like RNAs database Y2K. Nucleic Acids Res 2000;28:197-200.
11. Sinha S, Vasulu TS, De RK. Performance and evaluation of MicroRNA gene identification tools. J Proteom Bioinform 2009;2:336-43.
12. Borchert GM, Lanier W, Davidson BL. RNA polymerase III transcribes human microRNAs. Nat StructMol Biol 2006; 13:1097-101.
13. Jiang P, Wu H, Wang W, et al. MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res 2007;35:W339-44.
14. Eaves HL, Gao Y. MOM: maximum oligonucleotide mapping. Bioinformatics 2009;25:969-70.
15. Berezikov E, Guryev V, van de Belt J, et al. Phylogenetic shadowing and computational identification of human microRNA genes. Cell 2005;120:21-4.
16. Mendes ND, Freitas AT, Sagot MF. Current tools for the identification of miRNA genes and their targets. Nucleic Acids Res 2009;37:2419-33.
17. Friedlander MR, Chen W, Adamidi C, et al. Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 2008;26:407-15.
18. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009;10(3):R25.
19. Bonnet E, Wuyts J, Rouze P, Van de Peer Y. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 2004;20(17):2911-7.
20. Friedlander MR, Mackowiak SD, Li N, et al. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res 2012;40(1):37-52.
21. Mackowiak SD. Identification of novel and known miRNAs in deep-sequencing data with miRDeep2. In: Baxevanis AD, et al, (ed). Current Protocols in Bioinformatics. Chapter 12, Unit 12.10. John E Wiley and Sons, 2011.
22. Hackenberg M, Sturm M, Langenberger D, et al. miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res 2009;37:W68-76.
23. Hackenberg M, Rodriguez-Ezpeleta N, Aransay AM. miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments. Nucleic Acids Res 2011;39(Web Server issue):W132-8.
24. Huang P, Liu Y, Lee C, et al. DSAP: deep-sequencing small RNA analysis pipeline. NucleicAcidsRes 2010;38:W385-91.
25. Rice P, Longden I, Bleasby A. EMBOSS: the European molecular biology open software suite. Trends Genet 2000; 16(6):276-7.
26. Vaz C, Ahmad HM, Sharma P, et al. Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood. BMCGenom 2010;11:288-306.
27. Griffiths-Jones S, Saini HK, van Dongen S, et al. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008;36: D154-8.
28. Thakur V, Wanchana S, Xu M, et al. Characterization of statistical features for plant microRNA prediction. BMC Genom 2011;12:108-20.
29. de Hoon MJ, Taft RJ, Hashimoto T, et al. Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Res 2010; 20:257-64.
30. Guo L, Liang T, Gu W, et al. Cross-mapping events in miRNAs reveal potential miRNA-mimics and evolutionary implications. PloS One 2011;6:e20517-24.
31. Palmieri N, Schlotterer C. Mapping accuracy of short reads from massively parallel sequencing and the implications for quantitative expression profiling. PloS One 2009;4: e6323-33.
32. Otto TD, Sanders M, Berriman M, Newbold C. Iterative correction of reference nucleotides (iCORN) using second generation sequencing technology. Bioinformatics 2010;26: 1704-7.
33. Zhu E, Zhao F, Xu G, Hou H, Zhou L, Li X, et al. mirTools: microRNA profiling and discovery based on high-throughput sequencing. Nucleic Acids Res 2010; 38(Web Server issue):W392-7.
34. Farazi TA, Horlings HM, Ten Hoeve JJ, et al. MicroRNA sequence and expression analysis in breast tumors by deep sequencing. Cancer Res 2011;71(13):4443-53.
35. Creighton CJ, Reid JG, Gunaratne PH. Expression profiling of microRNAs by deep sequencing. Brief Bioinform 2009;10(5):490-7.
36. Howard BE, Heber S. Towards reliable isoform quantification using RNA-SEQ data. BMC Bioinform 2010; 11(Suppl 3):S6.