Descripción
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The purpose of this chapter is to introduce the reader to some of the most popular bioinformatics tools and resources available for RNA analysis. The introduction of RNA next-generation sequencing led to an explosion in the amount of quantitative transcript sequence data, which necessitated the development of adequate tools to process and make a sense of these rich and complex datasets. A large number of programs, platforms, and databases dedicated to RNA analysis have been produced over the past approximately 20 years; however, like so much other bioinformatics software, only a small portion of them are still available and in-use. As such, we will focus only on those tools and applications still in common use. This chapter is composed of three sections: the description of the general protocols for RNA sequence (generically called RNA-Seq) analyses, an outline of the most common approaches to map polyadenylation sites, and a brief introduction to noncoding RNA (ncRNA) analysis. The first section will describe the composition of steps within a typical RNA-Seq study: the experimental design, the sequencing methods, the data quality control, the read mapping, and the differential expression analysis. The second section will introduce a few recent methods developed to map polyadenylation sites: the experimental protocols (which are variations of RNA-Seq), polyadenylation site databases and prediction programs, and cis-regulatory elements discovery. The third and final section will present several of the ncRNA databases and prediction tools. | |
Internacional
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Si |
DOI
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10.1007/978-3-319-05687-6_15 |
Edición del Libro
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Editorial del Libro
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Springer International Publishing |
ISBN
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978-3-319-05686-9 |
Serie
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Título del Libro
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Fungal RNA Biology |
Desde página
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361 |
Hasta página
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391 |