MicroRNAs (miRNAs) are small, non-coding RNA (~20-22 nucleotides) that negatively regulate gene expression at post-transcriptional level. Accumulating evidence indicates that miRNAs play crucial roles in various physiological and pathological processes, such as development and tumorigenesis. Therefore, identification of comprehensive sets and differentially expressed miRNAs across tissues and cell lines becomes quite a hot area of study right now in solving a lot of the problems of gene regulation.

To comprehensive characterize the small RNA transcriptome, the appearance of 'deep-sequencing' technologies, such as Roche 454 and Illumina Solexa, have a number of significant advantages in comparison with previous hybridization-based methodologies, such as microarray or PCR-based assays. Firstly, it provides a more integrated view of the miRNAs transcriptome. With the added sequencing depth, high-throughput sequencing have an ability to identify modest or even low abundance miRNAs exhibiting expression differences between different samples, which can not be detected previously. Secondly, direct sequencing also offers the potential to detect variation in mature miRNA length and enzymatic modification of miRNAs. Thirdly, high-throughput sequencing allows the successful discovery of novel miRNAs, which need not rely on querying candidate regions of the genome but rather can be achieved by direct observation and validation of the folding potential of flanking genomic sequence. Taken together, next-generation sequencing technologies offer a highly robust, accurate and scalable system that sets a new standard for productively, cost-effectively investigation of small RNA transcriptome.

Although deep-sequencing schemes can generate millions of short sequences, they also 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 comprehensive characterizes the small RNA transcriptome.

The intention of mirTools:

• Classification of the large-scale short reads into known categories, such as known miRNAs, non-coding RNA, genomic repeats or coding sequences.

• Providing a detailed annotation information of known miRNAs, such as miRNA/miRNA*, absolute/relative reads count and the most abundant tag.

• Discovery of the novel miRNAs from the high-throughput sequencing technology.

• Identification of the differentially expressed miRNAs according to read tag counts (the number of reads for each tag reflects relative express level).