Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis

Nucleic Acids Research

Volumn 40, Issue 10, 2012, Pages 4298-4305

  Li, Yue ^a   Zhang, Zhuo ^b   Liu, Feng ^a   Vongsangnak, Wanwipa ^a   Jing, Qing ^b,c   Shen, Bairong ^a  

^a SOOCHOW UNIVERSITY   (China)

^b SECOND MILITARY MEDICAL UNIVERSITY   (China)

^c SHANGHAI JIAO TONG UNIVERSITY SCHOOL OF MEDICINE   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ACCURACY; ALGORITHM; ARTICLE; CAENORHABDITIS ELEGANS; COMPARATIVE STUDY; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; GALLUS GALLUS; GENE EXPRESSION PROFILING; HUMAN; HUMAN CELL; INFORMATION PROCESSING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA ANALYSIS; RNA SEQUENCE; SENSITIVITY ANALYSIS; SEQUENCE ANALYSIS; SPECIES DIFFERENTIATION;

ALGORITHMS; ANIMALS; CAENORHABDITIS ELEGANS; CHICK EMBRYO; GENE EXPRESSION PROFILING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICRORNAS; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, RNA; SOFTWARE; TIME FACTORS;

EID: 84861537341     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks043     Document Type: Article

References (18)

1. He, L. and Hannon, G.J. (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nat. Rev. Genet., 5, 522-531.
2. Lu, J., Getz, G., Miska, E.A., Alvarez-Saavedra, E., Lamb, J., Peck, D., Sweet-Cordero, A., Ebert, B.L., Mak, R.H., Ferrando, A.A. et al. (2005) MicroRNA expression profiles classify human cancers. Nature, 435, 834-838.
3. Brennecke, J., Stark, A., Russell, R.B. and Cohen, S.M. (2005) Principles of microRNA-target recognition. PLoS Biol., 3, e85.
4. Kim, V.N. and Nam, J.W. (2006) Genomics of microRNA. Trends Genet., 22, 165-173.
5. Lagos-Quintana, M., Rauhut, R., Lendeckel, W. and Tuschl, T. (2001) Identification of novel genes coding for small expressed RNAs. Science, 294, 853-858.
6. Wang, W.C., Lin, F.M., Chang, W.C., Lin, K.Y., Huang, H.D. and Lin, N.S. (2009) miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinformatics, 10, 328.
7. Zhu, E., Zhao, F., Xu, G., Hou, H., Zhou, L., Li, X., Sun, Z. and Wu, J. (2010) mirTools: microRNA profiling and discovery based on high-throughput sequencing. Nucleic Acids Res., 38, W392-W397.
8. Mathelier, A. and Carbone, A. (2010) MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data. Bioinformatics, 26, 2226-2234.
9. Friedlander, M.R., Chen, W., Adamidi, C., Maaskola, J., Einspanier, R., Knespel, S. and Rajewsky, N. (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat. Biotechnol., 26, 407-415.
10. Hackenberg, M., Sturm, M., Langenberger, D., Falcon-Perez, J.M. and Aransay, A.M. (2009) miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res., 37, W68-W76.
11. Hendrix, D., Levine, M. and Shi, W. (2010) miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data. Genome Biol., 11, R39.
12. Huang, P.J., Liu, Y.C., Lee, C.C., Lin, W.C., Gan, R.R., Lyu, P.C. and Tang, P. (2010) DSAP: deep-sequencing small RNA analysis pipeline. Nucleic Acids Res., 38, W385-W391.
13. Ronen, R., Gan, I., Modai, S., Sukacheov, A., Dror, G., Halperin, E. and Shomron, N. (2010) miRNAkey: a software for microRNA deep sequencing analysis. Bioinformatics, 26, 2615-2616.
14. Li, R., Yu, C., Li, Y., Lam, T.W., Yiu, S.M., Kristiansen, K. and Wang, J. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics, 25, 1966-1967.
15. Farrar, M. (2007) Striped Smith-Waterman speeds database searches six times over other SIMD implementations. Bioinformatics, 23, 156-161.
16. Smith, T.F. and Waterman, M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
17. Kuhn, R.M., Karolchik, D., Zweig, A.S., Wang, T., Smith, K.E., Rosenbloom, K.R., Rhead, B., Raney, B.J., Pohl, A., Pheasant, M. et al. (2009) The UCSC Genome Browser Database: update 2009. Nucleic Acids Res., 37, D755-D761.
18. Liang, H. and Li, W.H. (2009) Lowly expressed human microRNA genes evolve rapidly. Mol. Biol. Evol., 26, 1195-1198.