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PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data.

Personal-genomics endeavors, such as the 1000 Genomes project, are generating maps of genomic structural variants by analyzing ends of massively sequenced genome fragments. To process these we developed Paired-End Mapper (PEMer; http://sv.gersteinlab.org/pemer). This comprises an analysis pipeline, compatible with several next-generation sequencing platforms; simulation-based error models, yielding confidence-values for each structural variant; and a back-end database. The simulations demonstrated high structural variant reconstruction efficiency for PEMer's coverage-adjusted multi-cutoff scoring-strategy and showed its relative insensitivity to base-calling errors.

Pubmed ID: 19236709


  • Korbel JO
  • Abyzov A
  • Mu XJ
  • Carriero N
  • Cayting P
  • Zhang Z
  • Snyder M
  • Gerstein MB


Genome biology

Publication Data

January 19, 2009

Associated Grants

  • Agency: NCRR NIH HHS, Id: RR19895-02

Mesh Terms

  • Base Sequence
  • Computational Biology
  • Computer Simulation
  • Genome
  • Genomic Structural Variation
  • Genomics
  • Internet
  • Models, Genetic
  • Software