miRNAs are small, non-coding RNA that negatively regulate gene expression at post-transcriptional level, which play crucial roles in various physiological and pathological processes, such as development and tumorigenesis. Although deep sequencing technologies have been applied to investigate various small RNA transcriptomes, their computational methods are far away from maturation as compared to microarray-based approaches. In this study, a comprehensive web server mirTools was developed to allow researchers to comprehensively characterize small RNA transcriptome. With the aid of mirTools, users can: (i) filter low-quality reads and 3/5' adapters from raw sequenced data; (ii) align large-scale short reads to the reference genome and explore their length distribution; (iii) classify small RNA candidates into known categories, such as known miRNAs, non-coding RNA, genomic repeats and coding sequences; (iv) provide detailed annotation information for known miRNAs, such as miRNA/miRNA*, absolute/relative reads count and the most abundant tag; (v) predict novel miRNAs that have not been characterized before; and (vi) identify differentially expressed miRNAs between samples based on two different counting strategies: total read tag counts and the most abundant tag counts. We believe that the integration of multiple computational approaches in mirTools will greatly facilitate current microRNA researches in multiple ways. mirTools can be accessed at http://centre.bioinformatics.zj.cn/mirtools/ and http://22.214.171.124/mirtools.
Next-generation sequencing has been widely applied to understand the complexity of non-coding RNAs (ncRNAs) in a cost-effective way. In this study, we developed mirTools 2.0, an updated version of mirTools 1.0, which includes the following new features. (1) From miRNA discovery in mirTools 1.0, mirTools 2.0 allows users to detect and profile various types of ncRNAs, such as miRNA, tRNA, snRNA, snoRNA, rRNA, and piRNA. (2) From miRNA profiling in mirTools 1.0, mirTools 2.0 allows users to identify miRNA-targeted genes and performs detailed functional annotation of miRNA targets, including Gene Ontology, KEGG pathway and protein-protein interaction. (3) From comparison of two samples for differentially expressed miRNAs in mirTools 1.0, mirTools 2.0 allows users to detect differentially expressed ncRNAs between two experimental groups or among multiple samples. (4) Other significant improvements include strategies used to detect novel miRNAs and piRNAs, more taxonomy categories to discover more known miRNAs and a stand-alone version of mirTools 2.0. In conclusion, we believe that mirTools 2.0 (126.96.36.199/mr2_dev and centre.bioinformatics.zj.cn/mr2_dev) will provide researchers with more detailed insight into small RNA transcriptomes.
- mirTools: microRNA profiling and discovery based on high-throughput sequencing.,
, Nucleic Acids Res, 2010 Jul, Volume 38, Issue Web Server issue, p.W392-7, (2010)
- mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing.,
, RNA Biol, 2013 Jul, Volume 10, Issue 7, p.1087-92, (2013)