中草药相关文献

anneng

https://sci-hub.st/10.1007/s11816-019-00538-z
DNA barcoding in authentication of herbal raw materials, extracts
and dietary supplements: a perspective

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ＤＮＡ条形码技术应用于人参鉴定
DNA Barcoding Used in the Identification of Ginseng.pdf
相似性搜索法是一种基于ＢＬＡＳＴ搜索算法的鉴定
分析方法，来源于未知样品的ＤＮＡ条形码序列（ｑｕｅｒｙ
ｓｅｑｕｅｎｃｅ）与ＤＮＡ条形码数据库（ｒｅｆｅｒｅｎｃｅｌｉｂｒａｒｙ）进行
比对，如果在ＤＮＡ条形码数据库中找到完全一样的序
列（ｒｅｆｅｒｅｎｃｅｓｅｑｕｅｎｃｅ），那么未知样品就是该ｒｅｆｅｒｅｎｃｅ
ｓｅｑｕｅｎｃｅ对应的物种。对于人参鉴定而言，由于尚未有
正式的全球统一的ＤＮＡ条形码数据库，因此可直接将
条码序列与ＧｅｎＢａｎｋ数据库进行比对鉴定。
距离法是计算未知样品ＤＮＡ条形码序列（ｑｕｅｒｙ
ｓｅｑｕｅｎｃｅ）与数据库中每一个序列（ｒｅｆｅｒｅｎｃｅｓｅｑｕｅｎｃｅ）
的遗传距离，未知样品应为具有最小平均遗传距离
（ｍｅａｎｄｉｓｔａｎｃｅ）的物种或者具有最小遗传距离（ｎｅａｒｅｓｔ
ｄｉｓｔａｎｃｅ）的物种。Ｒｏｓｓ等建议使用Ｋ２Ｐ模型用于条形
码计算，可采用ＮｅｅｄｌｅｍａｎＷｕｎｓｃｈ动态规划算法进行
全局比对，计算两两序列的Ｋ２Ｐ距离，依据两种距离法
实施鉴定。
建树法是应用ＭＥＧＡ或ＰＡＵＰ等生物软件构建
ＮＪ、ＵＰＧＭＡ、ＭＰ等系统发育树，检验未知样品的ＤＮＡ
条形码序列（ｑｕｅｒｙｓｅｑｕｅｎｃｅ）与数据库中序列
（ｒｅｆｅｒｅｎｃｅｓｅｑｕｅｎｃｅ）聚类在一起的物种，根据聚类情
况进一步确定物种。Ｚｕｏ等［２６］
将测序所得人参属ＤＮＡ
条码序列用ＰＡＵＰ４．０软件进行聚类分析，通过聚类树
准确地将属内物种区分开，实现了人参的条码方法
鉴定。

anneng

http://www.gpgenome.com/
中国药材基因组数据库
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8354779/
the GPGD contains 21,872 DNA barcodes from 867 species, 2,203 organelle genomes from 674 species, 55 whole genomes from 49 species, 534 genomic sequencing datasets from 366 species, and 9,682 transcriptome datasets from 350 species.

anneng

http://herbalplant.ynau.edu.cn/#:~:text=Herbal Medicine Omics Database is,herbal plant effective components pathway.

anneng

https://treegenesdb.org/

anneng

http://cbcb.cdutcm.edu.cn/TCMPG/resource/genomes/
Although hundreds of medical plants have been sequenced, the related data were scattered at different sources, which hindered the systematical researches on medical plants. To solve such a challenge, we proposed the integrative database for Traditional Chinese Medicine Plant Genome (TCMPG). TCMPG not only deposits the genome data of traditional Chinese medical plants, but also provides a series of computational tools for researchers to perform systematical analysis. At present, 160 kinds of plants, 195 corresponding genomes, and 255 herbs (different parts from the same plant), together with the related information on plant species, genomes, and herbal medicines were included in TCMPG.
Moreover, the main genomic analysis tools, namely the BLAST to find orthologs from different plant, SSR Finder to identify SSRs, JBrowse to browse genomes, Synteny Viewer to display the syntenic blocks between two genomes, and HmmSearch to identify protein domain, were also embedded in TCMPG, which will facilitate the systematical analysis on medical plants. Once new data was reported, TCMPG will be updated and improved in time.