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MsLDR-creator: a web service to design msLDR assays

Abstract

MsLDR-creator is a free web service to design assays for the new DNA methylation detection method msLDR. The service provides the user with all necessary information about the oligonucleotides required for the measurement of a given CpG within a sequence of interest. The parameters are calculated by the nearest neighbour approach to achieve optimal behaviour during the experimental procedure. In addition, to guarantee a good start using msLDR, further information, like protocols and hints and tricks, are provided.

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References

  1. Bormann F, Sers C et al (2011) Methylation-specific ligation detection reaction (msLDR): a new approach for multiplex evaluation of methylation patterns. Mol Genet Genomics 286(3–4):279–291

  2. Borodina TA, Lehrach H et al (2004) Ligation detection reaction-TaqMan procedure for single nucleotide polymorphism detection on genomic DNA. Anal Biochem 333(2):309–319

  3. Haas S, Vingron M et al (1998) Primer design for large scale sequencing. Nucleic Acids Res 26(12):3006–3012

  4. SantaLucia J Jr (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA 95(4):1460–1465

  5. Sugimoto N, Nakano S et al (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res 24(22):4501–4505

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Author information

Correspondence to Felix Bormann.

Additional information

MsLDR-creator is available as web interface at: http://msldr.sys-bio.net.

Communicated by S. Hohmann.

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Bormann, F., Dahl, A. & Sers, C. MsLDR-creator: a web service to design msLDR assays. Mol Genet Genomics 287, 273–274 (2012). https://doi.org/10.1007/s00438-012-0677-9

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Keywords

  • msLDR
  • DNA-methylation
  • Epigenetics
  • Webservice
  • Multiplex
  • Universal TaqMan