CPSS 2.0: a computational platform update for the analysis of small RNA sequencing data

Abstract Summary Next-generation sequencing has been widely applied to understand the complexity of non-coding RNAs (ncRNAs) in the last decades. Here, we present CPSS 2.0, an updated version of CPSS 1.0 for small RNA sequencing data analysis, with the following improvements: (i) a substantial increase of supported species from 10 to 48; (ii) improved strategies applied to detect ncRNAs; (iii) more ncRNAs can be detected and profiled, such as lncRNA and circRNA; (iv) identification of differentially expressed ncRNAs among multiple samples; (v) enhanced visualization interface containing graphs and charts in detailed analysis results. The new version of CPSS is an efficient bioinformatics tool for users in non-coding RNA research. Availability and implementation CPSS 2.0 is implemented in PHP + Perl + R and can be freely accessed at http://114.214.166.79/cpss2.0/. Supplementary information Supplementary data are available at Bioinformatics online.

[1]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[2]  Anton J. Enright,et al.  Human MicroRNA Targets , 2004, PLoS biology.

[3]  Michael Hackenberg,et al.  sRNAtoolbox: an integrated collection of small RNA research tools , 2015, Nucleic Acids Res..

[4]  Qinghua Shi,et al.  mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing , 2013, RNA biology.

[5]  Peter F. Stadler,et al.  ViennaRNA Package 2.0 , 2011, Algorithms for Molecular Biology.

[6]  Huan Zhang,et al.  DeAnnIso: a tool for online detection and annotation of isomiRs from small RNA sequencing data , 2016, Nucleic Acids Res..

[7]  Gregory J. Goodall,et al.  A network-biology perspective of microRNA function and dysfunction in cancer , 2016, Nature Reviews Genetics.

[8]  Yanqing Wang,et al.  Bioinformatics Applications Note Databases and Ontologies Waprna: a Web-based Application for the Processing of Rna Sequences , 2022 .

[9]  Wei Yang,et al.  ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data , 2014, Bioinform..

[10]  André Fischer,et al.  Oasis: online analysis of small RNA deep sequencing data , 2015, Bioinform..

[11]  Anton J. Enright,et al.  Chimira: analysis of small RNA sequencing data and microRNA modifications , 2015, Bioinform..

[12]  Yu Xue,et al.  CPSS: a computational platform for the analysis of small RNA deep sequencing data , 2012, Bioinform..

[13]  Davide Heller,et al.  STRING v10: protein–protein interaction networks, integrated over the tree of life , 2014, Nucleic Acids Res..

[14]  Jihoon Kim,et al.  MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure , 2014, Bioinform..