title: ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data.
abstract: Integrative Short Reads NAvigator (ISRNA) is an online toolkit for analyzing high-throughput small RNA sequencing data. 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.
  
  
  BACKGROUND
  ISRNA is implemented in Java/C++/Perl/MySQL and can be freely accessed at http://omicslab.genetics.ac.cn/ISRNA/.
authors.affiliation: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and Graduate University of Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Guan-Zheng
authors.initials: GZ
authors.lastname: Luo
authors.forename: Wei
authors.initials: W
authors.lastname: Yang
authors.forename: Ying-Ke
authors.initials: YK
authors.lastname: Ma
authors.forename: Xiu-Jie
authors.initials: XJ
authors.lastname: Wang
mesh_terms: D002874:Chromosome Mapping; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D020407:Internet; D035683:MicroRNAs / Q000737:chemistry; D058727:RNA, Small Untranslated / Q000737:chemistry*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D035683:MicroRNAs; D058727:RNA, Small Untranslated