Analysis Tools
for small-RNA Deep Sequencing
LINUX/UNIX BASED TOOLS
Discovering microRNAs from deep sequencing data
using miRDeep
Nature Biotechnology (2008) 26 (4), pp. 407-415
MIRExpress:
Analyzing high-throughput sequencing data for profiling microRNA expression
BMC Bioinformatics (2009) 10, art. no. 1471, pp.
328 .
SeqBuster,
a bioinformatic tool for the processing and analysis of small RNAs datasets,
reveals ubiquitous miRNA modifications in human
embryonic cells.
Nucleic acids research (2010) 38 (5), pp. e34
MIReNA:
Finding microRNAs with high accuracy and no learning at genome scale and from
deep sequencing data
Bioinformatics (2010) 26 (18), art. no. btq329,
pp. 2226-2234
WEB-BASED TOOLS
miRanalyzer:
A microRNA detection and analysis tool for next-generation sequencing
experiments
Nucleic Acids Research (2009) 37 (SUPPL. 2), pp.
W68-W76 *
(http://web.bioinformatics.cicbiogune.es/microRNA/miRanalyser.php)
DSAP:
deep-sequencing small RNA analysis pipeline
Nucleic Acids Research. (2010) 38(Web Server
issue): W385–W391
(http://dsap.cgu.edu.tw/)
mirTools:
microRNA profiling and discovery based on high-throughput sequencing
Nucleic Acids Research. (2010) 38(Web Server
issue): W392–W397
(http://centre.bioinformatics.zj.cn/mirtools/)
