Abstract
The traditional Chinese medicine (TCM) genome project aims to reveal the genetic information and regulatory network of herbal medicines, and to clarify their molecular mechanisms in the prevention and treatment of human diseases. Moreover, the TCM genome could provide the basis for the discovery of the functional genes of active ingredients in TCM, and for the breeding and improvement of TCM. The traditional Chinese Medicine Basic Local Alignment Search Tool (TCM-Blast) is a web interface for TCM protein and DNA sequence similarity searches. It contains approximately 40G of genome data on TCMs, including protein and DNA sequence for 36 TCMs with high medical value.The development of a publicly accessible TCM genome alignment database hosted on the TCM-Blast website (http://viroblast.pungentdb.org.cn/TCM-Blast/viroblast.php) has expanded to query multiple sequence databases to obtain TCM genome data, and provide user-friendly output for easy analysis and browsing of BLAST results. The genome sequencing of TCMs helps to elucidate the biosynthetic pathways of important secondary metabolites and provides an essential resource for gene discovery studies and molecular breeding. The TCMs genome provides a valuable resource for the investigation of novel bioactive compounds and drugs from these TCMs under the guidance of TCM clinical practice. Our database could be expanded to other TCMs after the determination of their genome data.
Highlights
Whole-genome sequencing of the plants that form the basis of traditional Chinese medicine (TCM) is an important means for gene discovery and cultivation, synthetic biology, drug discovery and molecular breeding involving TCMs [1,2,3,4]
Overview of TCM‐Blast We have developed TCM-Blast, a web-based database for TCM genome alignment (Fig. 1)
TCM-Blast offers an interface to choose from TCM genome databases including TCM protein and Deoxyribonucleic acid (DNA) sequence datasets, which provide query functions with BLAST implementation [40]
Summary
Whole-genome sequencing of the plants that form the basis of traditional Chinese medicine (TCM) is an important means for gene discovery and cultivation, synthetic biology, drug discovery and molecular breeding involving TCMs [1,2,3,4]. Construction and content Genome data of TCMs were originated from the Herbal Medicine Omics Database (http://herbalplant.ynau.edu.cn/html/Genomes/), the Medicinal Plant Genomics Resource (http://medicinalplantgenomics.msu.edu), and the BIG Data Center in Beijing Institute of Genomics, Chinese Academy of Sciences (http://bigd.big.ac.cn/gsa/statistics). The TCM genome data used in TCM-Blast were collected from the Herbal Medicine Omics Database (http://herbalplant.ynau.edu.cn/html/Genomes/), the Medicinal Plant Genomics Resource (http://medicinalplantgenomics.msu.edu), and the BIG Data Center in Beijing Institute of Genomics (http://bigd.big.ac.cn/gsa/statistics) (the further details on the genome data sources for the thirty-six TCMs, see Table 1). These data resources have been published in professional journals and plant gene databases by academic institutions or government departments merged with plant gene databases, with abundant data sources and reliable data quality. In addition to other data resources, this database in our study has the following advantages: 1) this database is currently the largest Chinese medicine genome database; 2) this database includes the plant genetic data of Chinese medicine sources; and 3) this database provides support for the TCM breeding, cultivation of TCMs and the discovery of active ingredients in TCMs
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