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Multimedia Tools and Applications

, Volume 74, Issue 16, pp 6465–6480 | Cite as

PSIM: pattern-based read simulator for RNA-seq analysis

  • Sang-min LeeEmail author
  • Haesung Tak
  • Kiejung Park
  • Hwan-Gue Cho
  • Do-Hoon LeeEmail author
Article
  • 216 Downloads

Abstract

Next-generation sequencing technologies (NGS) require mapping tools that are fundamental for their application. These are evaluated by the level of accuracy to be matched and read at the original location. Evaluation increases the need for a simulator to generate reads with their locations and errors, as with indel. In this paper, we propose a simulator, PSIM, that generating a set of artificial RNA segments(reads) with the expression level and errors based on a pattern-based SAM file. PSIM adopts the contour line transpose and interval section shuffle methods to generate a similar expression level. In addition, we show the similarity between a profile contour of synthesized data and a reference sequence.

Keywords

RNA-seq Read simulator Bioinformatics 

Notes

Acknowledgments

This research was supported by a grant from the KRIBB Research Initiative Program.

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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  1. 1.Department of Computer Science and EngineeringPusan National UniversityBusanKorea
  2. 2.Korea Research Institute Bioscience and Biotechnology (KRIBB)DaejeonKorea
  3. 3.Korea Institute of Ocean Science and TechnologyAnsanKorea

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