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Ensembl

脊椎动物基因组浏览器

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Ensembl是一个脊椎动物基因组的基因组浏览器,支持比较基因组学、进化、序列变异和转录调控的研究。Ensembl注解基因,计算多种校准,预测调节功能和收集疾病数据。
Ensembl工具包括BLAST, BLAT, BioMart和变异效应预测器(VEP)为所有支持的物种。
BioMart是强大的RNA 在线ID转换工具;
BLAST是序列相似性搜索工具,可用于DNA和蛋白质。BLAT是默认的工具,因为它的速度更快。
Variant Effect Predictor: 分析自己的变体,并预测已知和未知变体的功能变化。

Ensembl 的特点:1、物种种类齐全。2、提供物种基因组序列。3、有比对工具:BLAST, BLAT, BioMart和变异效应预测器(VEP)。

Ensembl提供搜索功能,种类包括Gene, Transcript, Variant, Phenotype, Structural variation, Somatic mutation, Protein families, Gene tree, GenomicAlignment, Translation, Protein domains, Clones and regions, Marker.

提供物种数据的大类:
Protein-coding and non-coding genes, splice variants, cDNA and protein sequences, non-coding RNAs.
其中FASTA files for genes, cDNAs, ncRNA, proteins GTF or GFF3 files for genes, cDNAs, ncRNA, proteins

其中cDNA是互补DNA,是由mRNA反转录来的DNA,不包括ncRNA.双链DNA缩写是dsDNA,ncRNA表示非编码RNA.
CDS是编码序列(Coding sequence)的缩写。DNA转录成mRNA,mRNA经剪接等加工后翻译出蛋白质,所谓CDS就是与蛋白质序列一 一对应的DNA序列

以alt结尾的参考基因组文件,这个文件的alt代表:Alternate loci,不同的单倍体型,里面有不同的HLA序列,基因在一条染色体上的组合称单元型(haplotype ,又称单倍型)

作者:花色匆匆
链接:https://www.jianshu.com/p/ab947d540ebe
来源:简书
著作权归作者所有。商业转载请联系作者获得授权,非商业转载请注明出处。

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