Results 311 to 320 of about 2,805,364 (358)

M5: A Whole Genome Bacterial Encoder at Single Nucleotide Resolution

arXiv.org
A linear attention mechanism is described to extend the context length of an encoder only transformer, called M5 in this report, to a multi-million single nucleotide resolution foundation model pretrained on bacterial whole genomes.
Ágúst S. Egilsson
semanticscholar   +1 more source

Bacterial Genome Annotation

2012
Annotation of prokaryotic sequences can be separated into structural and functional annotation. Structural annotation is dependent on algorithmic interrogation of experimental evidence to discover the physical characteristics of a gene. This is done in an effort to construct accurate gene models, so understanding function or evolution of genes among ...
Nicholas, Beckloff, Shawn, Starkenburg, Tracey, Freitas, Patrick, Chain   +3 more
openaire   +2 more sources

Comparative genomics: the bacterial pan-genome

Current Opinion in Microbiology, 2008
Bacterial genome sequencing has become so easy and accessible that the genomes of multiple strains of more and more individual species have been and will be generated. These data sets provide for in depth analysis of intra-species diversity from various aspects.
Hervé, Tettelin, David, Riley, Ciro, Cattuto, Duccio, Medini   +3 more
openaire   +2 more sources

Bacterial Genome Sequencing

2009
For over 30 yr, the Sanger method has been the standard for DNA sequencing. Instruments have been developed and improved over time to increase throughput, but they always relied on the same technology. Today, we are facing a revolution in DNA sequencing with many drastically different platforms that have become or will soon become available on the ...
Hervé, Tettelin, Tamara, Feldblyum
openaire   +2 more sources

Bacterial Genome Reengineering

2011
The web application PrimerPair at ecogene.org generates large sets of paired DNA sequences surrounding- all protein and RNA genes of Escherichia coli K-12. Many DNA fragments, which these primers amplify, can be used to implement a genome reengineering strategy using complementary in vitro cloning and in vivo recombineering. The integration of a primer
Jindan, Zhou, Kenneth E, Rudd
openaire   +2 more sources

The Organization of the Bacterial Genome

Annual Review of Genetics, 2008
Many bacterial cellular processes interact intimately with the chromosome. Such interplay is the major driving force of genome structure or organization. Interactions take place at different scales—local for gene expression, global for replication—and lead to the differentiation of the chromosome into organizational units such as operons, replichores ...
openaire   +2 more sources

Evolution of bacterial genomes

Antonie van Leeuwenhoek, 1997
This review examines evolution of bacterial genomes with an emphasis on RNA based life, the transition to functional DNA and small evolving genomes (possible plasmids) that led to larger, functional bacterial genomes.
openaire   +2 more sources

Retrons, msDNA, and the bacterial genome

Cytogenetic and Genome Research, 2005
Retrons are distinct DNA sequences that code for a reverse transcriptase (RT) similar to the RTs produced by retroviruses and other types of retroelements. Retron DNAs are commonly associated with prophage DNA and are found in the genomes of a wide variety of different bacteria. The retron RT is used to synthesize a strange satellite DNA known as msDNA.
Lampson, B. C., Inouye, M., Inouye, S.
openaire   +3 more sources

IS elements as constituents of bacterial genomes

Research in Microbiology, 1999
We provide here an overview of our present understanding of the distribution of different insertion sequences (ISs) within bacterial genomes (both chromosomes and plasmids). This is at present fragmentary and a significant effort is needed in the analysis of the increasing number of genomes whose sequence has been determined.
J, Mahillon, C, Léonard, M, Chandler
openaire   +2 more sources

Bacterial genomics of plant adaptation

Nature Genetics, 2017
What allows bacteria, both pathogens and mutualists alike, to survive in close association with a eukaryotic host? A new study performed a large-scale comparative genomics analysis to identify novel genetic and genomic traits that are enriched in plant-associated bacterial taxa.
Ryan A, Melnyk, Cara H, Haney
openaire   +2 more sources