AI Article Synopsis

  • The chapter outlines a framework for analyzing small RNA (sRNA) in filamentous fungi, focusing on three main protocols: comparative analysis in different conditions, comparisons with RNAseq data, and identifying specialized sRNAs like methylguanosine-capped and polyadenylated sRNAs.
  • The study highlights the significance of these sRNAs in *Magnaporthe oryzae*, as they are associated with transcription start and end sites of protein-coding genes.
  • While specific command lines aren't provided, the chapter includes a general methodology, useful references, websites, and screenshots from a custom interface to help guide readers through the analysis process.

Article Abstract

The goal of this chapter is to provide a framework of sequential steps for small RNA (sRNA) analysis in filamentous fungi. Here, we present protocols for (1) comparative analysis of sRNAs in different conditions, (2) comparisons of sRNA libraries to RNAseq data and (3) identification and analysis of methylguanosine-capped and polyadenylated sRNAs (CPA-sRNAs). This species of small RNA is particularly interesting in Magnaporthe oryzae, as they map to transcription start and end sites of protein-coding genes. While we do not provide specific command lines for scripts, we provide a general framework for steps needed to carry out all three types of analyses, including relevant references, websites and free online tools. Screenshots are provided from our own customized interface using M. oryzae as an example, to assist the reader in visualizing many of the steps.

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Source
http://dx.doi.org/10.1007/978-1-4939-8724-5_5DOI Listing

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