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

Summary: Next generation sequencing (NGS) techniques have been widely used to document the small RNAs implicated in a variety of biological, physiological and pathological processes. An integrated computational tool is needed for handling and analyzing the enormous data sets from small RNA deep sequencing approach. Here 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 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: 1) 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, piRNAs and other non-coding small RNAs between paired samples, and detection of miRNA editing and modifications; 2) functional analysis, including prediction of miRNA targeted genes by multiple tools, enrichment of Gene Ontology terms (GO), signalling pathway involvement, and protein-protein interaction (PPI) analysis for the predicted genes. CPSS, a ready-to-use web server that integrates most functions of currently available bioinformatics tools, provides all the information wanted by the majority of users from small RNA deep sequencing data sets.

Availability: CPSS is implemented in PHP/PERL+MySQL+R and can be freely accessed at http://mcg.ustc.edu.cn/db/cpss/index.html orhttp://mcg.ustc.edu.cn/sdap1/cpss/index.html