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Bioinformatics. 2018 Oct 8. doi: 10.1093/bioinformatics/bty852. [Epub ahead of print]

sRNAPrimerDB: Comprehensive primer design and search web service for small non-coding RNAs.

Xie S1,2, Zhu Q3, Qu W4, Xu Z1, Liu X1,2, Li X1,2, Li S1, Ma W5, Miao Y1,2, Zhang L1, Du X3, Dong W6, Li H4, Zhao C1, Wang Y3, Fang Y3, Zhao S1,2.

Author information

Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, P. R. China.
The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, P. R. China.
Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China.
iGeneTech Bioscience Co., Ltd., Beijing, P. R. China.
Howard Hughes Medical Institute, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA.
College of Animal Science and Technology, Northwest A & F University, Yangling, P. R. China.



Small non-coding RNAs (ncRNAs), especially microRNAs (miRNAs) and piwi-interacting RNAs (piRNAs), play key roles in many biological processes. However, only a few tools can be used to develop the optimal primer or probe design for the expression profile of small ncRNAs. Here, we developed sRNAPrimerDB, the first automated primer designing and query web service for small ncRNAs.


The primer online designing module of sRNAPrimerDB is composed of primer design algorithms and quality evaluation of the polymerase chain reaction (PCR) primer. Five types of primers, namely, generic or specific reverse transcription primers, specific PCR primers pairs, TaqMan probe, double hairpin probe, and hybridization probe for different small ncRNA detection methods, can be designed and searched using this service. The quality of PCR primers is further evaluated using melting temperature, primer dimer, hairpin structure, and specificity. Moreover, the sequence and size of each amplicon are also provided for the subsequent experiment verification. At present, 531,306 and 2,941,669 primer pairs exist across 223 species for miRNAs and piRNAs, respectively, according to sRNAPrimerDB. Several primers designed by sRNAPrimerDB are further successfully validated by subsequent experiments.


sRNAPrimerDB is a valuable platform that can be used to detect small ncRNAs. This module can be publicly accessible at or

Supplementary information:

Supplementary data are available at Bioinformatics online.

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