The Gram-negative bacterium Xanthomonas euvesicatoria (Xcv) is the causal agent of bacterial spot disease in pepper and tomato. Xcv pathogenicity depends on a type III secretion (T3S) system that delivers effector proteins into host cells to suppress...
Journal of experimental zoology. Part B, Molecular and developmental evolution
26498580
The relationship between preferred codon use (PCU), developmental mode, and gene ontology (GO) was investigated in a sample of nine insect species with sequenced genomes. These species were selected to represent two distinct modes of insect developme...
Epigenetic factors are known to correlate with gene expression in the existing studies. However, quantitative models that accurately classify the highly and lowly expressed genes based on epigenetic factors are currently lacking. In this study, a new...
Prediction of essential genes helps to identify a minimal set of genes that are absolutely required for the appropriate functioning and survival of a cell. The available machine learning techniques for essential gene prediction have inherent problems...
BACKGROUND: High-throughput sequencing has made it theoretically possible to obtain high-quality de novo assembled genome sequences but in practice DNA extracts are often contaminated with sequences from other organisms. Currently, there are few exis...
Computational and mathematical methods in medicine
33133227
Enhancers are noncoding fragments in DNA sequences, which play an important role in gene transcription and translation. However, due to their high free scattering and positional variability, the identification and classification of enhancers have a h...
International journal of molecular sciences
32235762
The high density, large capacity, and long-term stability of DNA molecules make them an emerging storage medium that is especially suitable for the long-term storage of large datasets. The DNA sequences used in storage need to consider relevant const...
Promoter recognition is an important part of functional genomic annotation but a difficult problem. Many studies have been carried out to address this issue. However, they still cannot meet application needs. Most of the methods exhibit specificity, ...
DNA synthesis is widely used in synthetic biology to construct and assemble sequences ranging from short RBS to ultra-long synthetic genomes. Many sequence features, such as the GC content and repeat sequences, are known to affect the synthesis diffi...
MOTIVATION: Advances in bacterial promoter predictors based on machine learning have greatly improved identification metrics. However, existing models overlooked the impact of negative datasets, previously identified in GC-content discrepancies betwe...