miRNAkey: A software for microRNA deep sequencing analysis

Bioinformatics

Volumn 26, Issue 20, 2010, Pages 2615-2616

  Ronen, Roy ^a   Gan, Ido ^a   Modai, Shira ^a   Sukacheov, Alona ^b   Dror, Gideon ^b   Halperin, Eran ^a,c   Shomron, Noam ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b ACADEMIC COLLEGE OF TEL AVIV YAFFO   (Israel)

^c INTERNATIONAL COMPUTER SCIENCE INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ARTICLE; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; GENE EXPRESSION PROFILING; METHODOLOGY; NUCLEIC ACID DATABASE; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS;

BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; GENE EXPRESSION PROFILING; MICRORNAS; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 77957779549     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq493     Document Type: Article

References (14)

1. Bushati,N. and Cohen,S.M. (2007) microRNA functions. Annu. Rev. Cell Dev. Biol., 23, 175.
2. Calin,G.A. and Croce,C.M. (2006) MicroRNA signatures in human cancers. Nat. Rev. Cancer, 6, 857-866.
3. Friedländer,M.R. et al. (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat. Biotechnol., 26, 407-415.
4. Golan,D. et al. (2010) Biased hosting of intronic microRNA genes. Bioinformatics, 26, 992-995.
5. Hackenberg,M. (2009) miRanalyzer: A microRNA detection and analysis tool for next- generation sequencing experiments. Nucleic Acids Res., 37 (Web Server issue), W68-W76.
6. Huang,P.J., et al. (2010) DSAP: Deep-sequencing small RNAanalysis pipeline. Nucleic Acids Res., 38 (Suppl.), W385-W391.
7. Li,H. and Durbin,R. (2009) Fast and accurate short read alignment with Burrows- Wheeler transform. Bioinformatics, 25, 1754-1760.
8. Metzker,M.L. (2010) Sequencing technologies-the next generation. Nat. Rev. Genet., 11, 31-46.
9. Moxon,S. et al. (2008) A toolkit for analysing large-scale plant small RNA datasets. Bioinformatics, 24, 2252-2253.
10. Pantano,L. et al. (2010) SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNAmodifications in human embryonic cells. Nucleic Acids Res., 38, e34.
11. Pasaniuc,B. et al. (2010)Accurate estimation of expression levels of homologous genes in RNA-seq experiments. Proceedings of Research in Computational Molecular Biology: 14th Annual International Conference, RECOMB 2010, Lisbon, Portugal, August 12-15, pp. 397-407.
12. Shomron,N. et al. (2009) An evolutionary perspective of animal microRNAs and their targets. J. Biomed. Biotechnol., 2009, 594738.
13. Wang,W.C. et al. (2009) miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinformatics, 10,328.
14. Zhu,E. et al. (2010) mirTools: microRNA profiling and discovery based on high- throughput sequencing. Nucleic Acids Res., 38 (Suppl.), W392-W397.