Expression analysis and genome annotations with RNA sequencing

mRNA-Seq analysis with next-generation sequencing (NGS) provides large-scale gene expression profiles. Expression profile analysis against large-scale data permits us to discover novel genes with specific expression profiles. In this chapter, methods for mRNA-Seq analysis with NGS and large-scale expression analysis are introduced. It has become difficult to handle large-scale expression data by conventional statistical methods, such as hierarchical clustering method, as most of these methods for the large-scale expression data require long calculation times and substantial computer resources. Therefore, large-scale expression analysis methods that are efficiently and quickly executable without large computer resources are the main focus here. In addition, sequence analysis methods for mining single nucleotide polymorphisms (SNPs) with Genome-Seq are also shown here