A 1.11Gbp de novo assembly of the Lolium perenne genome was generated, containing 424,745 scaffolds and with N50 of 25,193. Gene prediction on genomic, mitochondrial and chloroplast scaffolds was carried out using both ab initio and RNA-Seq based methods. Ab initio gene prediction, carried out...
BUSCO - from QC to gene prediction and phylogenomics image.png C:完整的序列 S:单倍体拷贝 D:双倍体 F:打碎的 M:遗失的 n:总的片段个数 BUSCO“核心”基因数据库 image.png BUSCO pipeline image.png image.png 运行BUSCO image.png image.png 上面是我偷懒直接截图翻译的内容,凑合看吧hhh 一个好的基...
基因组从头测序(De novo sequencing)在不依赖参考基因组的情况下对某物种进行基因组测序及拼接组装,从而绘制该物种的全基因组 序列图谱。基因组测序不仅可以获得该物种的全基因组序列图谱,同时也为后续物种起源进化及特定环境适应性的研究奠定了基础。 根据基因组的复杂程度,基因组可分为 简单基因组和复杂基因组。
De novo gene prediction was performed using Genscan16 and Augustus17. A reference gene set was created by merging all of the gene sets. The sequencing reads were mapped on the panda genome sequence using SOAPaligner8, and heterozygous SNPs were identified by SOAPsnp9. Accession codes Data ...
Gene prediction and annotation Transcription factors annotation Noncoding RNAs annotation TE annotation Identification of homoeologous gene sets and orthologous gene sets Estimation of divergence time Phylogenetic tree construction and evolution rate estimation ...
基因组组装完成后,我们需要对我们组装好的基因组进行一个质量评估,质量评估主要从连续性(continuity),完整性(completeness),准确性( accuracy)3个方面来进行。连续性可以通过一些基本统计(contig/scaffold N50,total length,gap number等)和LAI指数来验证;完整性可以通过BUSCO和Merqury评估来验证;准确性可以通过Merqury的...
扬州大学农学院杨泽峰教授研究团队在Nature Communications期刊发表了题为“A de novo evolved gene contributes to rice grain shape difference betweenindicaandjaponica”的研究论文,系统阐释了一个de novo起源新基因GSE9参与调控水稻籼/粳亚种间粒型的分化,并为水稻粒型的遗传改良提供了新的靶基因。
The challenge of function prediction has interesting similarities and differences to the challenges of protein structure prediction.De-novostructure prediction was proven to be very hard10, requiring extensive resources11and reaching only limited success. Homology based structure prediction, on the other ha...
通过de novo预测来鉴定缺失的基因:MCScanX; 功能注释:BLASTP; 搜索蛋白质结构域:InterProScan; 筛选重复DNA序列:RepeatMasker; 结果: 1、 淀粉分离酵母KJJ81和KPH12的形态和基因组结构 ...
While there are a number of outstanding questions to be addressed in the field of de novo gene emergence, thematically they can be divided into two broad categories. The first debate centres on how non-coding regions of the genome acquire protein-coding capacity. This transition requires at a ...