mirTools

Web-Based Tools for MicroRNA Analysis from Deep Sequencing Data

by Chris on December 23, 2009

in Web Based Tools

mirTools – a web server for microRNA profiling and discovery based on high-throughput sequencing data.

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).

miRDeep – Discovering known and novel miRNAs from deep sequencing data

The miRDeep package was developed to discover active known or novel miRNAs from deep sequencing data (Solexa/Illumina, 454, …). The package consists of everything you need to analyze your own deep sequencing data after removal of ligation adapters: a number of scripts to preprocess the mapped data, and the core miRDeep algorithm that will analyze and score these data.

deepBase – a database for deeply annotating and mining deep sequencing data

a novel database, developed to facilitate the comprehensive annotation and discovery of small RNAs from transcriptomic data. The current release of deepBase contains deep sequencing data from 185 small RNA libraries from diverse tissues and cell lines of seven organisms: human, mouse, chicken, Ciona intestinalis, Drosophila melanogaster, Caenhorhabditis elegans and Arabidopsis thaliana. For the purpose of comparative analysis, deepBase provides an integrative, interactive and versatile display. A convenient search option, related publications and other useful information are also provided for further investigation. [click to continue…]

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