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mRNA/miRNA-seq technology is becoming the leading technology to globally profile gene expression and elucidate the transcriptional regulation mechanisms in living cells.Although there are many tools available for analyzing RNA-seq data, few of them are available as easy accessible online web tools for processing both mRNA and miRNA data for the RNA-seq based user community.As such, we have developed a comprehensive web application tool for processing mRNA-seq and miRNA-seq data.Our web tool wapRNA includes four different modules: mRNA-seq and miRNA-seq sequenced from SOLiD or Solexa platform and all the modules were tested on previously published experimental data.We accept raw sequence data with an optional reads filter, followed by mapping and gene annotation or miRNA prediction.wapRNA also integrates downstream functional analyses such as Gene Ontology, KEGG pathway, miRNA targets prediction and comparison of genes or miRNAs different expression in different samples.Moreover, we provide the executable packages for installation on users local server.Background: RNA-Seq is a recently developed revolutionary approach for transcriptome profiling and miRNA analysis using next generation sequencing technologies.It can allow us to study RNA in further depth and more accurate measurement.Studies using this method have already altered our view of transcriptome and miRNA.Recently, a lot of methods have been developed to process the different aspects of RNA-seq data, such as short reads mapping (Li and Durbin, 2009), gene annotation and differential gene-expression analysis (Wang, et al., 2010).Meanwhile, several web-services for RNA and microRNA analysis have also been developed, such as rQuant.web (Bohnert and Ratsch, 2010), MAGIA (Sales, et al., 2010), miRCat (Moxon, et al., 2008), miRAnalyzer (Hackenberg, et al., 2009), mirTools (Zhu, et al., 2010) and DSAP (Huang, et al., 2010).However, some of these web-services need prior data processing, such as mapping raw sequences, normalizing expression data, or they dont provide local installation package.In order to provide a service for the increasing amount of experimental studies using RNA-seq methods, here, we present the wapRNA, a novel web service that allows us to do mRNA and miRNA expression analysis simultaneously.wapRNA complements other RNA analysis tools reported by Goncalves et al.(Goncalves, et al., 2011).Moreover, we provide the executable packages for installation on users local server.This will facilitate studies for RNA using high-throughput approaches, especially for biologists who have limited computing sources or are short of bioinformatics processing experience.Methods: wapRNA consists of front-end and back-end programs.The front-end program, constructed based on Java Server Page (JSP) 2.0 technology, is in charge of tasks submission and results display.We used the Struts (http://struts.apache.org), Spring (http:// www.springsource.org) and Hibernate (http://www.hibernate.org/) framework to enhance the flexibility and extendibility, and Mysql5.0 as the DBMS to store the interim and final results.The back-end program consists of series of Perl and Shell scripts, it is mainly in charge of the data processing.Ten animal species whose genome sequences are available are provided in our server (The species will be added according to users requirements in future), and the gene structure information is based on ENSEMBL (http://asia.ensembl.org/index.html) annotation.Results: The wapRNA web service simplifies the analysis of mRNA-seq/miRNAseq data by executing a computational pipeline on a set of data uploaded by user.We built four modules for SOLiD mRNA, Solexa mRNA, SOLiD miRNA and Solexa miRNA data analysis respectively to accommodate different sequencing methods (SOLiD or Solexa) and study targets (RNA or miRNA).We also provide executable packages for users to build their pipeline locally.Conclusions: The wapRNA web service provides users to analyze next-generation sequencing mRNA and miRNA data directly and simply by an easy-to-use browser user interface.The service includes major processes for the next-generation mRNA or miRNA data analysis, including preprocessing raw sequenced reads, mapping tags to reference sequences, gene expression annotation, and other downstream functional analysis such as detecting differentially expressed genes, Gene Ontology and KEGG pathway analysis for RNA, novel miRNA predication and miRNA target prediction .