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Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...

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Related Experiment Video

Updated: Mar 12, 2026

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources

Published on: September 3, 2009

gargammel: a sequence simulator for ancient DNA.

Gabriel Renaud¹, Kristian Hanghøj^1,2, Eske Willerslev^1,3,4

¹Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark.

Bioinformatics (Oxford, England)

|November 1, 2016

Summary

This summary is machine-generated.

Gargammel simulates ancient DNA (aDNA) characteristics like fragmentation and damage in silico. This tool helps researchers assess potential impacts on their analyses of ancient genomic data.

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Last Updated: Mar 12, 2026

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Published on: September 3, 2009

Novel Sequence Discovery by Subtractive Genomics

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Design and Synthesis of a Reconfigurable DNA Accordion Rack

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Published on: August 15, 2018

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Ancient DNA (aDNA) analysis is crucial for understanding extinct species and past populations.
aDNA samples often exhibit fragmentation, damage, and contamination, complicating downstream analyses.
Simulating these characteristics is essential for accurate in silico analysis.

Purpose of the Study:

To develop a computational package for simulating ancient DNA fragments.
To enable researchers to assess the impact of aDNA characteristics on their analyses.
To reproduce common biases found in ancient DNA datasets.

Main Methods:

Developed 'gargammel', a package that simulates ancient DNA fragments.
The simulation models post-mortem DNA fragmentation, DNA damage, and experimental sequencing errors.
The package utilizes known reference genomes as input.

Main Results:

Gargammel accurately reproduces common biases observed in ancient DNA datasets.
The package simulates the entire molecular process from fragmentation to sequencing errors.
Provides a tool for in silico assessment of aDNA data quality.

Conclusions:

Gargammel offers a valuable tool for researchers working with ancient DNA.
The package aids in understanding and mitigating biases in aDNA analyses.
Facilitates more robust inferences from ancient genomic data.