Computational tool composites alternative way to identify essential genes and it is low-cost and time-efficient. Based on experimental essentiality sets deposited in the databases DEG and OGEE as reference, we developed an automatically computational tool named Geptop to select essential genes from the set of protein-coding genes in a prokaryotic genome, which utilizes the strategy of reciprocally best hit for homology search and evolutionary distance for weight assigning. The latest version of Geptop is 2.0 ( http://guolab.whu.edu.cn/geptop ), which can predict gene essentiality with the mean AUC 0f 0.84 in prokaryotes and is more stable. The chapter is to briefly introduce the tool and tell how to use it.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1007/978-1-0716-1720-5_23 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Chromosome-level genome assembly of black carp Mylopharyngodon piceus using Nanopore and Hi-C technologies.
Sci Data
January 2025
Department of Infectious Diseases and Public Health, City University of Hong Kong, Kowloon Tong, Hong Kong.
Black carp (Mylopharyngodon piceus) is one of the "four famous domestic fishes" in China and an important economic fish in freshwater aquaculture. A high-quality genome is essential for advancing future biological research and breeding programs for this species. In this study, we aimed to generate a high-quality chromosome-level genome assembly of black carp using Nanopore and Hi-C technologies.
View Article and Find Full Text PDFAnthracyclines disaggregate and restore mutant p63 function: a potential therapeutic approach for AEC syndrome.
Cell Death Discov
January 2025
Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA.
Ankyloblepharon-Ectodermal Defects-Cleft Lip/Palate (AEC) syndrome is a rare genetic disorder caused by mutations in the TP63 gene, which encodes a transcription factor essential for epidermal gene expression. A key feature of AEC syndrome is chronic skin erosion, for which no effective treatment currently exists. Our previous studies demonstrated that mutations associated with AEC syndrome lead to p63 protein misfolding and aggregation, exerting a dominant-negative effect.
View Article and Find Full Text PDFTime-series analysis reveals metabolic and transcriptional dynamics during mulberry fruit development and ripening.
Int J Biol Macromol
January 2025
Sericultural Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China; Institute of Special Economic Animal and Plant, Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China. Electronic address:
Understanding the global transcriptomic and metabolic changes during mulberry growth and development is essential for the enhancing fruit quality and optimizing breeding strategies. By integrating phenotypic, metabolomic, and transcriptomic data across 18 developmental and ripening stages of Da10 mulberry fruit, a global map of gene expression and metabolic changes was generated. Analysis revealed a gradual progression of morphological, metabolic, and transcriptional changes throughout the development and ripening phases.
View Article and Find Full Text PDFUbiquitination-dependent degradation of DHX36 mediated by porcine circovirus type 3 capsid protein.
Virology
January 2025
College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China. Electronic address:
Porcine circovirus type 3 (PCV3) is an emerging pathogen that causes porcine dermatitis, and reproductive failure. PCV3 Cap interacts with DExD/H-box helicase 36 (DHX36), a protein that functions primarily through regulating interferon (IFN)-β production. However, how the interaction between DHX36 and PCV3 Cap regulates viral replication remains unknown.
View Article and Find Full Text PDFComprehensive characterization of the bHLH transcription factor family in Curcuma wenyujin and functional elucidation of CwbHLH27 in jasmonate-regulated sesquiterpenoid biosynthesis.
Plant Physiol Biochem
January 2025
School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China; Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, 311121, China; School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai, 200030, China; Xinchang Pharmaceutical Factory, Zhejiang Medicine CO., LTD, China. Electronic address:
Curcuma wenyujin is acknowledged as a crucial medicinal plant containing essential oils, primarily composed of sesquiterpenoids. While numerous sesquiterpenoids exhibit versatile physiological activities, their levels in C. wenyujin are generally low, particularly the pivotal anti-cancer component elemene.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!