mirTools for microRNA profiling and discovery based on high-throughput sequencing
mirTools: a web server for microRNA profiling and discovery based on high-throughput sequencing
Although deep-sequencing schemes can be applied to unbiased, quantitive and in-depth investigation of the small RNA transcriptome that has been previously possible, they present substantial informatics challenges for lack of efficient and flexible tools to handle and analysis a huge scale of short sequences. Therefore, a comprehensive web server mirTools was developed to allow researchers to comprehensive characterizes the small RNA transcriptome. With the aid of mirTools, it can:
1) Align the large-scale short reads to the reference genome and exhibit the length distribution;
2) Classify of the large-scale short reads into known categories, such as known miRNAs, non-coding RNA, genomic repeats or coding sequences;
3) Provide detailed annotation information of known miRNAs, such as miRNA/miRNA*, absolute/relative reads count and the most abundant tag;
4) Discovery of the novel miRNAs that have not been characterized before from the large-scale short reads;
5) Identify of the differentially expressed miRNAs between samples according to different count strategies, such as total read tag counts and the most abundant tag of specific miRNA.
Zhu E, Zhao F, Xu G, Hou H, Zhou L, Li X, Sun Z, Wu J. mirTools: microRNA profiling and discovery based on high-throughput sequencing. Nucleic Acids Research. 2010
mirTools can be available at http://centre.bioinformatics.zj.cn/mirtools/.
Although deep-sequencing schemes can be applied to unbiased, quantitive and in-depth investigation of the small RNA transcriptome that has been previously possible, they present substantial informatics challenges for lack of efficient and flexible tools to handle and analysis a huge scale of short sequences. Therefore, a comprehensive web server mirTools was developed to allow researchers to comprehensive characterizes the small RNA transcriptome. With the aid of mirTools, it can:
1) Align the large-scale short reads to the reference genome and exhibit the length distribution;
2) Classify of the large-scale short reads into known categories, such as known miRNAs, non-coding RNA, genomic repeats or coding sequences;
3) Provide detailed annotation information of known miRNAs, such as miRNA/miRNA*, absolute/relative reads count and the most abundant tag;
4) Discovery of the novel miRNAs that have not been characterized before from the large-scale short reads;
5) Identify of the differentially expressed miRNAs between samples according to different count strategies, such as total read tag counts and the most abundant tag of specific miRNA.
Zhu E, Zhao F, Xu G, Hou H, Zhou L, Li X, Sun Z, Wu J. mirTools: microRNA profiling and discovery based on high-throughput sequencing. Nucleic Acids Research. 2010
mirTools can be available at http://centre.bioinformatics.zj.cn/mirtools/.
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