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Molecular Identity Check based on Complete Genome Data

Often the question arises if two or more cultures derived from the same strain are still identical. Classical identification approaches as MALDI-TOF, 16S analysis or even MLST only provide insufficient information as differences are usually matter of a few dozens to thousands genome-wide Single Nucleotide Polymorphisms (short SNPs).

Consequently, DSMZ now offers a new Bioinformatics Service, the "Molecular Identity Check". Hereby, the reference genome of choice is completely sequenced based on third generation sequencing technology. This includes the assembly of all replicons (chromosome and plasmids) and automated genome annotation via Prokka. One (or more) further strains for comparison will be sequenced based on short read data. An alignment of short read data to the reference genome via BWA with subsequent variant calling using VarScan generates a complete list of all SNPs compared to the reference strain. Based on given annotation the affected genes are listed.

Download the service order form here.

Dr. Cathrin Spröer

Senior scientist

References

  1. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014 Jul 15;30(14):2068-9. doi: 10.1093/bioinformatics/btu153. Epub 2014 Mar 18. PMID: 24642063.
  2. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18. PMID: 19451168; PMCID: PMC2705234.
  3. Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics. 2009 Sep 1;25(17):2283-5. doi: 10.1093/bioinformatics/btp373. Epub 2009 Jun 19. PMID: 19542151; PMCID: PMC2734323.