sRNAPrimerDB: comprehensive primer design and search web service for small non-coding RNAs
sRNAPrimerDB: comprehensive primer design and search web service for small non-coding RNAs
复制标题
sRNAPrimerDB：针对小非编码 RNA 的综合引物设计和搜索网络服务
DOI：
10.1093/bioinformatics/bty852
复制
发表时间：
2019-05-01
期刊：
影响因子：
5.8
通讯作者：
Zhao, Shuhong
中科院分区：
文献类型：
--
作者：
Xie, Shengsong;Zhu, Qin;Zhao, Shuhong
小分子非编码RNA（ncRNA），特别是microRNA（miRNAs）和piwi-interacting RNA（piRNAs），在许多生物学过程中起着关键作用。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。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（polymerase chain reaction，PCR）引物质量评价两部分组成。该服务可设计和检索5种引物，即通用或特异性逆转录引物、特异性PCR引物对、TaqMan探针、双发夹探针和杂交探针，用于不同的小ncRNA检测方法。使用解链温度、引物二聚体、发夹结构和特异性进一步评价PCR引物的质量。此外，还提供了每个扩增子的序列和大小，以供后续实验验证。目前，根据sRNAPrimerDB，在223个物种中分别存在531306和2941669对miRNAs和piRNAs引物对。sRNAPrimerDB设计的几种引物在后续实验中得到了进一步的成功验证。可用性和实施sRNAPrimerDB是一个有价值的平台，可用于检测小ncRNA。该模块可在http://www.srnaprimerdb.com或http://123.57.239.141.Supplementary信息上公开访问补充数据可在在线生物信息学上获取。
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, 531306 and 2941669 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 informationSupplementary data are available at Bioinformatics online.