Results 11 to 20 of about 171,414 (293)
Dynamic construction of pan-genome subgraphs [PDF]
Open Computer Science, 2020 Marcus et al. (Bioinformatics 2014) proposed to use a compressed de Bruijn graph as a description of a pan-genome, comprising the genomes of many individuals/strains of the same or closely related species. Subsequent work improved the construction of the
Dede Kadir, Ohlebusch Enno
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The pan-genome of Saccharomyces cerevisiae [PDF]
FEMS Yeast Research, 2019 ABSTRACT Understanding genotype–phenotype relationship is fundamental in biology. With the benefit from next-generation sequencing and high-throughput phenotyping methodologies, there have been generated much genome and phenome data for Saccharomyces cerevisiae. This makes it an excellent model system to understand the genotype–phenotype
Gang Li, Boyang Ji, Jens Nielsen
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Building a Pan-Genome Reference for a Population [PDF]
Journal of Computational Biology, 2015 Abstract A reference genome is a high quality individual genome that is used as a coordinate system for the genomes of a population, or genomes of closely related subspecies. Given a set of genomes partitioned by homology into alignment blocks we formalize the problem of ordering and orienting the blocks such that the resulting ...
Ngan Nguyen +8 more
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panX: pan-genome analysis and exploration [PDF]
Nucleic Acids Research, 2016 Horizontal transfer, gene loss, and duplication result in dynamic bacterial genomes shaped by a complex mixture of different modes of evolution. Closely related strains can differ in the presence or absence of many genes, and the total number of distinct genes found in a set of related isolates – the pan-genome – is often many times ...
Ding, Wei +2 more
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Pan-genome Search and Storage.
, 2018 High Throughput Sequencing (HTS) technologies are constantly improving and making genome sequencing more affordable. However, HTS sequencers can only produce short overlapping genome fragments that are erroneous and cover the sequenced genomes unevenly. These genome fragments are assembled based on their overlaps to produce larger contiguous sequences.
Holley, Guillaume
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Pan-Genome Storage and Analysis Techniques
, 2017 Computational pan-genome analysis has emerged from the rapid increase of available genome sequencing data. Starting from a microbial pan-genome, the concept has spread to a variety of species, such as plants or viruses. Characterizing a pan-genome provides insights into intra-species evolution, functions, and diversity.
Zekic, Tina +5 more
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Pan-Genome miRNomics in Brachypodium [PDF]
Plants, 2021 Pan-genomes are efficient tools for the identification of conserved and varying genomic sequences within lineages of a species. Investigating genetic variations might lead to the discovery of genes present in a subset of lineages, which might contribute into beneficial agronomic traits such as stress resistance or yield.
Tugdem Muslu +4 more
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Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs
Genome Biology, 2021 We present pandora, a novel pan-genome graph structure and algorithms for identifying variants across the full bacterial pan-genome. As much bacterial adaptability hinges on the accessory genome, methods which analyze SNPs in just the core genome have ...
Rachel M. Colquhoun +10 more
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The Salmonella enterica Pan-genome [PDF]
Microbial Ecology, 2011 Salmonella enterica is divided into four subspecies containing a large number of different serovars, several of which are important zoonotic pathogens and some show a high degree of host specificity or host preference. We compare 45 sequenced S. enterica genomes that are publicly available (22 complete and 23 draft genome sequences).
Jacobsen, Annika +4 more
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First Steps in the Analysis of Prokaryotic Pan-Genomes
Bioinformatics and Biology Insights, 2020 Pan-genome is defined as the set of orthologous and unique genes of a specific group of organisms. The pan-genome is composed by the core genome, accessory genome, and species- or strain-specific genes.
Sávio Souza Costa +4 more
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