sRNAPrimerDB：全面的小非编码 RNA 引物设计和搜索网络服务。

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

机构信息

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.

出版信息

Bioinformatics. 2019 May 1;35(9):1566-1572. doi: 10.1093/bioinformatics/bty852.

DOI:10.1093/bioinformatics/bty852

PMID:30295699

Abstract

MOTIVATION

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.

RESULTS

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.

AVAILABILITY AND IMPLEMENTATION

sRNAPrimerDB is a valuable platform that can be used to detect small ncRNAs. This module can be publicly accessible at http://www.srnaprimerdb.com or http://123.57.239.141.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

动机

小非编码 RNA（ncRNA），特别是 microRNA（miRNA）和 piwi 相互作用 RNA（piRNA），在许多生物过程中发挥着关键作用。然而，只有少数工具可用于开发小 ncRNA 表达谱的最佳引物或探针设计。在这里，我们开发了 sRNAPrimerDB，这是第一个用于小 ncRNA 的自动化引物设计和查询网络服务。

结果

sRNAPrimerDB 的引物在线设计模块由引物设计算法和聚合酶链反应（PCR）引物的质量评估组成。使用此服务，可以设计和搜索 5 种类型的引物，即通用或特定逆转录引物、特定 PCR 引物对、TaqMan 探针、双链探针和杂交探针，用于不同的小 ncRNA 检测方法。进一步使用熔解温度、引物二聚体、发夹结构和特异性评估 PCR 引物的质量。此外，还提供了每个扩增子的序列和大小，以便随后进行实验验证。目前，根据 sRNAPrimerDB，针对 miRNA 和 piRNA，分别在 223 个物种中存在 531306 和 2941669 对引物。通过 sRNAPrimerDB 设计的几个引物通过后续实验进一步得到验证。