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sRNAPrimerDB: comprehensive primer design and search web service for small non-coding RNAs
- Source :
- Bioinformatics. 35:1566-1572
- Publication Year :
- 2018
- Publisher :
- Oxford University Press (OUP), 2018.
-
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.
- Subjects :
- Statistics and Probability
Computer science
Computational biology
Polymerase Chain Reaction
Biochemistry
law.invention
03 medical and health sciences
law
Primer dimer
microRNA
TaqMan
Molecular Biology
Polymerase chain reaction
DNA Primers
030304 developmental biology
0303 health sciences
Hybridization probe
030302 biochemistry & molecular biology
RNA
Amplicon
Non-coding RNA
Reverse transcriptase
Computer Science Applications
Computational Mathematics
Computational Theory and Mathematics
RNA, Small Untranslated
Primer (molecular biology)
Algorithms
Software
Subjects
Details
- ISSN :
- 13674811 and 13674803
- Volume :
- 35
- Database :
- OpenAIRE
- Journal :
- Bioinformatics
- Accession number :
- edsair.doi.dedup.....55ac5bb7db4a818e42bc30dfeeb660f9