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DNA, Volume 2, Issue 2

2022 June - 3 articles

Cover Story: An essential step for many bioinformatics studies is to determine the order of nucleotides in a given genome. Conventional physical mapping methods, while very effective for genome assembly, are prohibitively expensive; instead, less-contiguous genome assemblies are built using whole-genome shotgun (WGS) sequencing data. Here, we introduce Physlr—a tool that constructs next-generation physical maps using WGS linked reads. Physlr leverages long-range information in linked reads to infer a chromosome-scale physical map in the form of an overlap graph of sequenced molecules. It can be used for various genomics analyses, including scaffolding. Here, we demonstrate how physical maps can be used to substantially improve genome assemblies over state-of-the-art linked-read scaffolding tools. View this paper

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Review

16 Citations

13,489 Views

18 Pages

Mitochondrial DNA: Consensuses and Controversies

Inna Shokolenko and
Mikhail Alexeyev

DNA2022, 2(2), 131-148;https://doi.org/10.3390/dna2020010

10 June 2022

In the course of its short history, mitochondrial DNA (mtDNA) has made a long journey from obscurity to the forefront of research on major biological processes. mtDNA alterations have been found in all major disease groups, and their significance rem...

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Article

4 Citations

4,119 Views

15 Pages

Physlr: Next-Generation Physical Maps

Amirhossein Afshinfard,
Shaun D. Jackman,
Johnathan Wong,
Lauren Coombe,
Justin Chu,
Vladimir Nikolic,
Gokce Dilek,
Yaman Malkoç,
René L. Warren and
Inanc Birol

DNA2022, 2(2), 116-130;https://doi.org/10.3390/dna2020009

10 June 2022

While conventional physical maps helped build most of the reference genomes we use today, generating the maps was prohibitively expensive, and the technology was abandoned in favor of whole-genome shotgun sequencing (WGS). However, genome assemblies...

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Article

1 Citations

6,738 Views

12 Pages

Updating the Phylogeography and Temporal Evolution of Mitochondrial DNA Haplogroup U8 with Special Mention to the Basques

Vicente M. Cabrera

DNA2022, 2(2), 104-115;https://doi.org/10.3390/dna2020008

7 April 2022

Mitochondrial DNA phylogenetic and phylogeographic studies have been very useful in reconstructing the history of modern humans. In addition, recent advances in ancient DNA techniques have enabled direct glimpses of the human past. Taking advantage o...

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