TGP-WEB:一个用于自动基因预测Trichoderma基因组的服务器
Li Zhang1, Housong Cui2, Song Yu3
1Hainan University, Haikou, China; 23210904000030@hainanu.edu.cn.
Phytopathology
|February 1, 2026
概括
特里科德玛基因预测网络服务器 (TGP-WEB) 为特里科德玛物种提供了准确的基因预测,有助于理解这些有益的微生物. 该工具为研究和分类学研究提供了全面的基因组.
科学领域:
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
- 菌类学 菌类学是指菌类学.
背景情况:
- 三体物种是植物有益的重要微生物和生物控制剂.
- 准确的基因预测对于理解Trichoderma基因组学和功能至关重要.
- 现有的基因预测工具可能缺乏Trichoderma的特异性或效率.
研究的目的:
- 开发和介绍Trichoderma基因预测Web服务器 (TGP-WEB),用于准确地预测Trichoderma基因组中的基因.
- 为研究人员提供一个用户友好的平台,以获得全面的基因组和功能注释.
- 为了促进基因组研究和Trichoderma物种的分类学澄清.
主要方法:
- 混合基因预测策略结合了*ab initio* (奥古斯都,GeneMark) 和基于同质 (Braker) 的方法.
- 使用排名框架整合和优先考虑预测.
- 通过域注释和BUSCO对完整性的评估进行功能评估.
- 利用NCBI Refseq数据库中的真菌蛋白序列进行基于同质性的预测.
主要成果:
- 在177个Trichoderma基因组的基因预测中,TGP-WEB实现了高准确性.
- 基准测试显示,在88%的已发表基因组中,基因恢复率>90%.
- 为135个以前没有注释的基因组生成了完整的基因组.
- 根据BUSCO的评估,94.92%的基因组的完整性高于97%.
- 能够识别2100个单拷贝基因以进行强大的遗传学分析.
结论:
- 在Trichoderma基因组中,TGP-WEB是一个准确而高效的基因预测工具.
- 产生的基因组和遗传学分析增强了对Trichoderma分类学和进化的理解.
- TGP-WEB将支持对这些重要真菌物种的持续研究.
相关概念视频
Genome Size and the Evolution of New Genes
9.1K
While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
9.1K
Genome Size and the Evolution of New Genes
3.4K
3.4K
Genomics
40.7K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
40.7K
Automatic Processing and Automatic Social Behavior
253
Automatic processing refers to the cognitive operations that occur without conscious intent or awareness, playing a fundamental role in shaping social cognition and behavior. These processes enable individuals to navigate complex social environments efficiently by relying on mental shortcuts and pre-existing knowledge structures known as schemas. One of the most influential mechanisms underlying automatic processing is priming, which subtly activates mental representations through exposure to...
253
Genomic Imprinting and Inheritance
37.2K
Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
The expression of some genes depends on which parent passed the gene to the offspring, through a phenomenon known as...
The expression of some genes depends on which parent passed the gene to the offspring, through a phenomenon known as...
37.2K
Predicting Molecular Geometry
45.8K
VSEPR Theory for Determination of Electron Pair Geometries
45.8K


