Sorting genomes with rearrangements and segmental duplications through trajectory graphs
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Simple Summary:& nbsp;After domestication in specific regions, livestock followed human migrations and colonized the whole world. During this population expansion, human and natural selection, together with demographic events, molded the livestock genome l ...
Nodular thelitis is a chronic enzootic infection affecting dairy cows and goats. The causative agent was recently shown to be related to the leprosy-causing bacilli Mycobacterium leprae and Mycobacterium lepromatosis. In this study, the genome of this path ...
Advances in high‐throughput sequencing have promoted the collection of reference genomes and genome‐wide diversity. However, the assessment of genomic variation among populations has hitherto mainly been surveyed through single‐nucleotide polymorphisms (SN ...
Complete genomes can be recovered from metagenomes by assembling and binning DNA sequences into metagenome assembled genomes (MAGs). Yet, the presence of microdiversity can hamper the assembly and binning processes, possibly yielding chimeric, highly fragm ...
A fundamental problem in comparative genomics is to compute the distance between two genomes in terms of its higher level organization (given by genes or syntenic blocks). For two genomes without duplicate genes, we can easily define (and almost always eff ...
Many important questions in molecular biology, evolution, and biomedicine can be addressed by comparative genomic approaches. One of the basic tasks when comparing genomes is the definition of measures of similarity (or dissimilarity) between two genomes, ...
Background: The gene family-free framework for comparative genomics aims at providing methods for gene order analysis that do not require prior gene family assignment, but work directly on a sequence similarity graph. We study two problems related to the b ...
Motivation: Large-scale evolutionary events such as genomic rearrange. ments and segmental duplications form an important part of the evolution of genomes and are widely studied from both biological and computational perspectives. A basic computational pro ...
A fundamental problem in comparative genomics is to compute the distance between two genomes. For two genomes without duplicate genes, we can easily compute a variety of distance measures in linear time, but the problem is NP-hard under most models when ge ...
The Desulfitobacterium genus comprises anaerobic Gram-positive bacteria, of which the majority are facultative organohalide respirers. We here present the genomes of eight strains of Desulfitobacterium spp., including five strains of Desulfitobacterium haf ...
