title: IsomiR Bank: a research resource for tracking IsomiRs.
abstract: : Next-Generation Sequencing (NGS) technology has revealed that microRNAs (miRNAs) are capable of exhibiting frequent differences from their corresponding mature reference sequences, generating multiple variants: the isoforms of miRNAs (isomiRs). These isomiRs mainly originate via the imprecise and alternative cleavage during the pre-miRNA processing and post-transcriptional modifications that influence miRNA stability, their sub-cellular localization and target selection. Although several tools for the identification of isomiR have been reported, no bioinformatics resource dedicated to gather isomiRs from public NGS data and to provide functional analysis of these isomiRs is available to date. Thus, a free online database, IsomiR Bank has been created to integrate isomiRs detected by our previously published algorithm CPSS. In total, 2727 samples (Small RNA NGS data downloaded from ArrayExpress) from eight species (Arabidopsis thaliana, Drosophila melanogaster, Danio rerio, Homo sapiens, Mus musculus, Oryza sativa, Solanum lycopersicum and Zea mays) are analyzed. At present, 308 919 isomiRs from 4706 mature miRNAs are collected into IsomiR Bank. In addition, IsomiR Bank provides target prediction and enrichment analysis to evaluate the effects of isomiRs on target selection.
  
  
  
  IsomiR Bank is implemented in PHP/PERL + MySQL + R format and can be freely accessed at http://mcg.ustc.edu.cn/bsc/isomir/
  
  
  
  : aoli@ustc.edu.cn or qshi@ustc.edu.cn
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei 230027, Anhui, China.
authors.forename: Yuanwei
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: School of Information Science and Biology, Centers for Biomedical Engineering, University of Science and Technology of China, Hefei 230027, China.
authors.forename: Qiguang
authors.initials: Q
authors.lastname: Zang
authors.affiliation: Reproductive Medical Centre of Anhui, Provincial Hospital Affiliated to Anhui Medical University, Hefei 230001, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Xu
authors.affiliation: Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei 230027, Anhui, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Zheng
authors.affiliation: School of Information Science and Biology, Centers for Biomedical Engineering, University of Science and Technology of China, Hefei 230027, China.
authors.forename: Rongjun
authors.initials: R
authors.lastname: Ban
authors.affiliation: Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei 230027, Anhui, China.
authors.forename: Huan
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Department of Statistics, University of Kentucky, Lexington, KY 40536, USA and.
authors.forename: Yifan
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei 230027, Anhui, China.
authors.forename: Qiaomei
authors.initials: Q
authors.lastname: Hao
authors.affiliation: Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei 230027, Anhui, China.
authors.forename: Furhan
authors.initials: F
authors.lastname: Iqbal
authors.affiliation: School of Information Science and Biology, Centers for Biomedical Engineering, University of Science and Technology of China, Hefei 230027, China.
authors.forename: Ao
authors.initials: A
authors.lastname: Li
authors.affiliation: Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei 230027, Anhui, China, Hefei Institute of Physical Science, China Academy of Science, Hefei 230027, China.
authors.forename: Qinghua
authors.initials: Q
authors.lastname: Shi
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D010944:Plants / Q000235:genetics
chemical_list: D035683:MicroRNAs