Polyadenylation in Plants pp 25-37

Part of the Methods in Molecular Biology book series (MIMB, volume 1255) | Cite as

Extraction of Poly(A) Sites from Large-Scale RNA-seq Data

Protocol

Abstract

The NCBI manages the SRA (Sequence Read Archive) database to store RNA-Seq data generated from different NGS technologies. With ever increasing finished and ongoing genome and transcriptome sequencing projects, the data in SRA expand rapidly and present a treasure for mining useful information to facilitate our understanding of biological issues like mRNA 3′-end formation and alternative polyadenylation. We developed a bioinformatics pipeline that can process raw SRA sequence data and obtain high quality poly(A) sites and poly(A) cluster sites with detailed expression information. This pipeline is designed to be generic and can be utilized for polyadenylation studies in any eukaryotic species.

Key words

Polyadenylation RNA-Seq SRA Poly(A) site Data mining 

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Department of AutomationXiamen UniversityXiamenChina
  2. 2.Department of BiologyMiami UniversityOxfordUSA
  3. 3.Department of Computer Science and Software EngineeringMiami UniversityOxfordUSA

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