Updates

Welcome to EMPOP 4

EMPOP now uses the new developed query engine SAM2 (Huber et al. 2018) that is based on SAM( Röck et al. (2010))

 

Overview of EMPOP 4 and SAM 2

  • phylogenetic alignment of a mitotype in contrast to the input alignment. The phylogenetic principle follows the rules developed in Bandelt and Parson 2008 that are meanwhile generally accepted in the forensic community (SWGDAM 2013 , ISFG 2014). Thus alignment and notation of mitotypes can be standardized within the forensic genetic community and also in other fields of research.
  • estimated haplogroup status based on Phylotree nomenclature (van Oven and Kayser 2009). Details will be provided in a separate publication (Huber et al. in prep)
  • Updated alignment/nomenclature conventions for instable (length variant) regions 50-70, 310-316, 455-460, 961-966, 8276-8279, 16180-16193, and 16258-16262
  • catalogue of 28 block indels that are considered as single variant/difference to comply with the phylogenetic interpretation of mitotypes
  • updated catalogue of length variant regions that can be excluded from the database search
  • search function for neighbours by phylogenetic costs

Refinement of Haplogroup Assignment

The tolerance level of EMMA was downsized from 0.3 to 0.1 to allow for a finer haplogroup estimation of mtDNA haplotypes. Extensive testing on a data set comprising 86,048 haplotypes suggested that this reduction would be beneficial for forensically relevant haplogrouing. Especially haplotypes previously assigned to haplogroups H, L3 and M benefit from a more accurate classification.

Welcome to EMPOP 3

EMPOP 3 represents a new mtDNA database version based on a novel programming concept and website layout. New features are included to accommodate Massively Parallel (Next Generation) Sequencing data.

Good things that remain

  • EMPOP only holds high quality mtDNA sequence data that underwent stringent quality control
  • EMPOP uses SAM, an alignment-free search engine to guarantee that matches are found regardless of the alignment and nomenclature of query and database haplotypes
  • MtDNA haplotypes are sorted by geographic and metapopulation categories that are relevant to forensics and informative for other scientific fields

New developments in EMPOP 3

  • The earlier distinction in forensic and literature data is no more required, as the QC tools applied to every uploaded dataset proved to be effective and reliable
  • Tabular summaries of query results are presented in a more convenient format
  • Statistical evaluation of matching haplotypes was improved by offering correction for sampling bias
  • Neighbors are presented by Hamming distance and by costs (fluctuation rate)
  • Haplogroup estimates of mtDNA sequences are provided based on maximum likelihood/minimum cost functions
  • Geographical maps are provided to present the distribution of matching haplotypes and the distribution of haplogroups
  • Haplogroup Browser is a new tool to search for and display the distribution of mitochondrial haplogroups

DrawNetWork updated to v1.25

Minor improvements regarding the layout when exporting networks in SVG and EPS format have been made. Detailed haplotypes of nodes are shown in a sortable table now.

Release 11 is online, N=34617

We have updated the database with 1.427 new haplotypes from 4 different countries (Chile, Portugal, Spain, USA).