The localization of a protein in a cell is closely correlated with its biological function. With the explosion of protein sequences entering into DataBanks, it is highly desired to develop an automated method that can fast identify their subcellular location. This will expedite the annotation process, providing timely useful information for both basic research and industrial application. In view of this, a powerful predictor has been developed by hybridizing the gene ontology approach [Nat. Genet. 25 (2000) 25], functional domain composition approach [J. Biol. Chem. 277 (2002) 45765], and the pseudo-amino acid composition approach [Proteins Struct. Funct. Genet. 43 (2001) 246; Erratum: ibid. 44 (2001) 60]. As a showcase, the recently constructed dataset [Bioinformatics 19 (2003) 1656] was used for demonstration. The dataset contains 7589 proteins classified into 12 subcellular locations: chloroplast, cytoplasmic, cytoskeleton, endoplasmic reticulum, extracellular, Golgi apparatus, lysosomal, mitochondrial, nuclear, peroxisomal, plasma membrane, and vacuolar. The overall success rate of prediction obtained by the jackknife cross-validation was 92%. This is so far the highest success rate performed on this dataset by following an objective and rigorous cross-validation procedure.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1016/j.bbrc.2004.06.073 | DOI Listing |
BMC Plant Biol
January 2025
Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 520521, China.
Background: Calmodulin-binding transcription activator (CAMTA) proteins play significant roles in signal transduction, growth and development, as well as abiotic stress responses, in plants. Understanding their involvement in the low-temperature stress response of teak is vital for revealing cold resistance mechanisms.
Results: Through bioinformatics analysis, the CAMTA gene family in teak was examined, and six CAMTA genes were identified in teak.
Poult Sci
December 2024
Guangdong Province Key Laboratory of Livestock Disease Prevention, Key Laboratory of Avian Infuenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Afairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China. Electronic address:
Avian coccidiosis, caused by protozoan parasites of the genus Eimeria, is a globally prevalent and highly pathogenic disease that poses a serious threat to the poultry industry, resulting in significant economic losses. However, the mechanism by which Eimeria species invade host cells remains unclear. Previous studies have identified rhoptry neck protein 2 (RON2) from Eimeria tenella as a critical factor in host cell invasion, but a comprehensive understanding of the role of EtRON2 in host cell invasion and its relationship with E.
View Article and Find Full Text PDFMicroorganisms
December 2024
College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China.
Corn leaf blight and stem rot caused by are significant diseases that severely affect corn crops. Glycosyltransferases (GTs) catalyze the transfer of sugar residues to diverse receptor molecules, participating in numerous biological processes and facilitating functions ranging from structural support to signal transduction. This study identified 101 genes through functional annotation of the TZ-3 genome.
View Article and Find Full Text PDFSpatial transcriptomics (ST) provides critical insights into the complex spatial organization of gene expression in tissues, enabling researchers to unravel the intricate relationship between cellular environments and biological function. Identifying spatial domains within tissues is essential for understanding tissue architecture and the mechanisms underlying various biological processes, including development and disease progression. Here, we present Randomized Spatial PCA (RASP), a novel spatially aware dimensionality reduction method for spatial transcriptomics (ST) data.
View Article and Find Full Text PDFPlant Sci
January 2025
Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China. Electronic address:
The stripe color of watermelon is a vital commercial trait and is the focus of attention of consumers and researchers. However, the genetic determinants of watermelon stripe color are incompletely understood. Based on the results of preliminary localization studies, we constructed a large-capacity F generation population (710 plants) using light-green striped ZXG1555 and green-striped Cream of Saskatchewan (COS) watermelon strains as parental lines for fine mapping.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!