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ISRNA | An integrative online toolkit for short reads from high-throughput sequencing data


A piece of online software designed for storage, visualization and analysis of small RNA sequencing data produced by high-throughput sequencing technologies. Besides the high-speed genome mapping function, ISRNA provides statistics for genomic location, length distribution and nucleotide composition bias analysis of sequence reads. Number of reads mapped to known microRNAs and other classes of short non-coding RNAs, coverage of short reads on genes, expression abundance of sequence reads as well as some other analysis functions are also supported. The versatile search functions enable users to select sequence reads according to their sub-sequences, expression abundance, genomic location, relationship to genes, etc. A specialized genome browser is integrated to visualize the genomic distribution of short reads. ISRNA also supports management and comparison among multiple datasets.

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ISRNA classification

ISRNA specifications

Unique identifier:
Web user interface
Programming languages:
C++, Java, Perl
Computer skills:
Integrative Short Reads NAvigator
Restrictions to use:
Database management system:

ISRNA support


  • Xiu-Jie Wang <>


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State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; Graduate University of Chinese Academy of Sciences, Beijing, China

Funding source(s)

This work was supported by the grants from the Ministry of Science and Technology of China (number 2011CBA01101), the 863 program of China (2011AA020108) and the Chinese Academy of Sciences (numbers XDA01020105 and KSCX2-EW-R-01-03).

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