MicroHapDB

MicroHapDB is a comprehensive catalog of human microhaplotype variation. The database integrates marker and population frequency data from numerous published research articles—see citations. Allele frequency estimates and allelic diversity statistics (\(A_e\)) are computed for 26 global populations so that markers can be ranked and evaluated for various applications.

MicroHapDB is designed to be user-friendly for researchers, technology developers, and forensic practitioners, supporting a range of access methods from browsing and simple text queries to complex queries and full programmatic access via a Python API. It is designed as a community resource requiring minimal infrastructure to use and maintain: the entire contents of the database are distributed in plain text with each copy of MicroHapDB.

Table of Contents

• Getting started
  • Command line interface
  • Python API
  • Direct file access
• Installation
  • Overview
  • Development quick start
  • Extending or rebuilding the database
• Ranking markers
• Configuring marker target sequences
  • Delta: flanking sequence
  • L: minimum length criterion
  • E: extend mode
  • CLI Example
  • Impacted outputs
• Adding Markers to MicroHapDB
• Citations
  • Supporting software
  • Ranking statistics
  • Published marker collections and allele frequency data

If you use this database, please cite our work.

• Standage DS, Mitchell RN (2020) MicroHapDB: A Portable and Extensible Database of All Published Microhaplotype Marker and Frequency Data. Frontiers in Genetics 11:781, doi:10.3389/fgene.2020.00781.

MicroHapDB was created and is maintained by the Bioinformatics Group at the National Bioforensic Anaylsis Center (NBFAC). Contact: daniel.standage@st.dhs.gov.

Reference: command line interface

• microhapdb population
• microhapdb marker
• microhapdb frequency
• microhapdb lookup

Indices and tables

• Index

• Module Index

• Search Page