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Nucleic Acids Res. 2016 Jul 8;44(W1):W166-75. doi: 10.1093/nar/gkw427. Epub 2016 May 13.

DeAnnIso: a tool for online detection and annotation of isomiRs from small RNA sequencing data.

Author information

1
Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China Hefei Institute of Physical Science, China Academy of Science, Hefei 230027, China.
2
School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China.
3
Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China.
4
Department of statistics, University of Kentucky, Lexington, KY 40536, USA.
5
Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan 60800, Pakistan.
6
School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China Research Centers for Biomedical Engineering, University of Science and Technology of China, Hefei 230027, China aoli@ustc.edu.cn.
7
Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China Hefei Institute of Physical Science, China Academy of Science, Hefei 230027, China qshi@ustc.edu.cn.

Abstract

Small RNA (sRNA) Sequencing technology has revealed that microRNAs (miRNAs) are capable of exhibiting frequent variations from their canonical sequences, generating multiple variants: the isoforms of miRNAs (isomiRs). However, integrated tool to precisely detect and systematically annotate isomiRs from sRNA sequencing data is still in great demand. Here, we present an online tool, DeAnnIso (Detection and Annotation of IsomiRs from sRNA sequencing data). DeAnnIso can detect all the isomiRs in an uploaded sample, and can extract the differentially expressing isomiRs from paired or multiple samples. Once the isomiRs detection is accomplished, detailed annotation information, including isomiRs expression, isomiRs classification, SNPs in miRNAs and tissue specific isomiR expression are provided to users. Furthermore, DeAnnIso provides a comprehensive module of target analysis and enrichment analysis for the selected isomiRs. Taken together, DeAnnIso is convenient for users to screen for isomiRs of their interest and useful for further functional studies. The server is implemented in PHP + Perl + R and available to all users for free at: http://mcg.ustc.edu.cn/bsc/deanniso/ and http://mcg2.ustc.edu.cn/bsc/deanniso/.

PMID:
27179030
PMCID:
PMC4987950
DOI:
10.1093/nar/gkw427
[Indexed for MEDLINE]
Free PMC Article

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