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...n in large-scale small RNA datasets (12). miRanalyzer is a web server tool that can detect all known miRNA sequences annotated in miRBase and predict novel miRNAs based on a machine-learning approach =-=(13)-=-. UEA small RNA tools were designed to the analysis of high-throughput small RNA data, such as identification of miRNAs and their targets, and comparison expression levels in specific small RNA loci (...

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...es and the two libraries were compared for differential expression of the sequences using the Fisher’s exact test with Bonferroni’s correction. Sequences were deemed significantly differentially expressed by the two libraries if the p-value was ,0.001 and there was at least a 2–fold change in the sequences’ normalized counts. Novel miRNA identification The sequences that did not match known miRNA stem-loop sequences were filtered out with known transcripts sequences downloaded from UCSC [17]. To identify novel miRNA candidates amongst the remaining unmatched sequences, the miRanalyzer program [18] was used (http://web.bioinformatics. cicbiogune.es/microRNA/miRanalyser.php). The output candidates were checked one by one for homologies to known noncoding RNA, and non-homologous sequences were taken as novel miRNA candidates. miRNA target prediction and pathway analysis The target genes for each differentially expressed miRNA were predicted using MicroCosm version 5 [19,20] with a threshold of p = 0.001. As some of the genes were potentially regulated by both up-regulated and down-regulated miRNAs, we focused for further analysis on the genes that were potentially regulated only by upregu...

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...ct (7,8) at a low abundance. Since the application of NGS to miRNA detection, many sequencing software tools have been developed to support miRNA data analysis. These include miRDeep (9), miRanalyzer =-=(10)-=-, miRExpress (6), miRTRAP (11), DSAP (12), mirTools (7), MIReNA (8), miRNAkey (13) and mireap which can be accessed at http://sourceforge .net/projects/mireap/. miRDeep and mireap were early software ...

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...o 6 aresdiscarded. The sequences with greater copy number in the remaining pairedssequences are the mature sequences.sEliminating Coding RNAs and Distinguishing the Novel and Conserved miRNAssBLASTX (=-=Hackenberg et al., 2009-=-; Hendrix et al., 2010) is introduced forsaligning the mature sequences to the NCBI database. The sequences with highspossibilities translated to protein are eliminated, and the E-value here aresrestr...

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...n in large-scale small RNA datasets (12). miRanalyzer is a web server tool that can detect all known miRNA sequences annotated in miRBase and predict novel miRNAs based on a machine-learning approach =-=(13)-=-. UEA small RNA tools were designed to the analysis of high-throughput small RNA data, such as identification of miRNAs and their targets, and comparison expression levels in specific small RNA loci (...

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...an be finished in 15 min. Comparison with other similar applications Identification and profiling of miRNA with NGS technology is a relatively new approach. Only three other applications, miRanalyzer =-=(29)-=-, miRExpress (30) and miRDeep (31) are available for the analysis of miRNA deep-sequencing datasets. miRanalyzer is a web server tool that performs small RNA classification and new miRNA prediction bu...

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...mall RNA-seq data contain a plethora of processing and maturation products potentially including yet unknown RNA species. Despite this fact, many small RNA-seq data analysis tools such as miRanalyzer =-=(11)-=-, miRDeep (12) or miRNAkey (13) focus on microRNAs—largely neglecting other types of RNAs. In addition, these programs are often restricted to specific sequencing platforms due to embedded mapping alg...

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...enesis (11). MIReNA uses combinatorial rules to identify miRNAs (12). miRanalyzer uses a support vector machine (SVM) trained on miRNA features to classify miRNA transcripts from nonmiRNA transcripts =-=(13,14)-=-. miRTRAP identifies gene loci where many sequenced RNAs map to few defined positions (15). Evaluation of these algorithms is however difficult since they have each only been tested on a limited numbe...