Research Based On RNA-seq Alternative Splice Prediction Algorithm

Pre-mRNA splicing is a complex and ubiquitous nuclear process that is a natural source of carcinogenic errors in gene expression.In addition,many studies over the past 20 years have reported cancer-specific alternative splicing in the absence of genomic mutations.Affected proteins include transcription factors,cellular signal transducers and components of the extracellular matrix.Antibodies against alternative splicing products on cancer cells are currently undergoing clinical trials,and competitive reverse transcription PCR across alternative splicing regions was used as a simple diagnostic test.In addition to being associated with cancer,the nature of the surrogate gene product is often consistent with the positive role in cancer;therefore,the alternative splicing process itself is a potential target for gene therapy.So the main work of this article is as follows:(1)With the rapid growth of a large number of DNA sequences,gene prediction has become a problem in bioinformatics.Splice site prediction plays a key role in gene identification.Therefore,it is of great significance to develop a new method for improving the prediction accuracy of splice junctions.By combining RF with the three most recent encoding methods(MM1,MM2,and MCM),we have demonstrated that the proposed method performs roughly the same as the SVM-based method and is generally better.In addition,the proposed method is simple,rapid,easy to use and can be applied to large-scale human genome data to identify splice sites.As a future study,these methods can also be used to identify other regulatory regions,such as translation initiation sites and promoters.(2)Although the list of known alternative splicing events has been increasing since then,new isomers are usually observed in disease situations or when working in large populations.Given that the identification of intact isoforms is technically challenging or expensive,focusing on single splicing events as a surrogate for transcriptome properties is fruitful for a wide range of analyses.We provide SplAdder,a new method for large-scale analysis of alternative splicing events based on RNA-Seq data.SplAdder has been successfully applied to the splicing analysis of various organisms,showing a high degree of overall accuracy compared to other advanced methods,and can be easily applied to thousands of sample data sets.We are working hard to further improve SplAdder to natively handle high-performance computing clusters and generate more interactive visualizations.(3)We have identified many genes that are differentially spliced between normal and cancerous tissues.Most experimentally validated tissue-specific alternative splicing events occur in genes involved in cytoskeletal architecture,extracellular matrix or cell-cell interactions.Some of these events report splice variants that occur in a tissue-specific manner and may represent loss of tissue function rather than help with transformation or metastasis due to dedifferentiation of the colonic epithelium and smooth muscle cells.Determining the role of these splicing events requires more detailed studies,but in most cases these genes have previously been implicated in the activity of tumor progression.