CPSS: a computational platform for the analysis of small RNA deep sequencing data

Bioinformatics
Yuanwei ZhangQinghua Shi

Abstract

Next generation sequencing (NGS) techniques have been widely used to document the small ribonucleic acids (RNAs) implicated in a variety of biological, physiological and pathological processes. An integrated computational tool is needed for handling and analysing the enormous datasets from small RNA deep sequencing approach. Herein, we present a novel web server, CPSS (a computational platform for the analysis of small RNA deep sequencing data), designed to completely annotate and functionally analyse microRNAs (miRNAs) from NGS data on one platform with a single data submission. Small RNA NGS data can be submitted to this server with analysis results being returned in two parts: (i) annotation analysis, which provides the most comprehensive analysis for small RNA transcriptome, including length distribution and genome mapping of sequencing reads, small RNA quantification, prediction of novel miRNAs, identification of differentially expressed miRNAs, piwi-interacting RNAs and other non-coding small RNAs between paired samples and detection of miRNA editing and modifications and (ii) functional analysis, including prediction of miRNA targeted genes by multiple tools, enrichment of gene ontology terms, signalling pathway involvem...Continue Reading

References

Apr 9, 2008·Nature Biotechnology·Marc R FriedländerNikolaus Rajewsky
Oct 23, 2008·Nucleic Acids Research·Lars J JensenChristian von Mering
Feb 26, 2009·Cell·Richard W Carthew, Erik J Sontheimer
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Mar 26, 2011·Bioinformatics·Yuanwei ZhangQinghua Shi
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Sep 8, 2011·Bioinformatics·Wenming ZhaoSongnian Hu
Dec 3, 2011·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Linglin ZhouJinyu Wu

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Citations

Jun 5, 2014·BMC Genomics·Zhifu SunJean-Pierre Kocher
Jun 8, 2014·Bioinformatics·Jihoon KimLucila Ohno-Machado
May 7, 2016·Bioinformatics·Yuanwei ZhangQinghua Shi
Jun 4, 2015·Cellular and Molecular Life Sciences : CMLS·Fabian Afonso-Grunz, Sören Müller
Jul 15, 2015·Journal of Translational Medicine·Christina BackesAndreas Keller
Jun 20, 2015·Frontiers in Bioengineering and Biotechnology·Dario VenezianoAlfredo Ferro
Feb 24, 2015·Bioinformatics·Vincenzo CapeceStefan Bonn
May 17, 2018·BMC Research Notes·Pamela H RussellKaterina Kechris
Jul 18, 2017·Frontiers in Plant Science·Junyang YueYongsheng Liu
Mar 24, 2017·Briefings in Functional Genomics·Vaibhav ShuklaKapaettu Satyamoorthy
Jul 3, 2018·Database : the Journal of Biological Databases and Curation·Huan ZhangQinghua Shi
Jul 12, 2019·F1000Research·Lorena PantanoShannan Ho Sui

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