廣州市黃埔區(qū)學(xué)大道攬?jiān)侣窂V州企業(yè)孵化器B座402
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1.2 生物信息學(xué)相關(guān)數(shù)據(jù)庫
生物信息學(xué)數(shù)據(jù)庫可以分為4大類:即基因組數(shù)據(jù)庫、核酸和蛋白質(zhì)一級(jí)結(jié)構(gòu)數(shù)據(jù)庫、生物大分子三維空間結(jié)構(gòu)數(shù)據(jù)庫，當(dāng)前研究比較熱點(diǎn)的集中于基因組、miRNA、LncRNA、circRNA等分子的查詢，以及蛋白或蛋白修飾變化（甲基化、乙?；龋┡cDNA啟動(dòng)子、miRNA、LncRNA、circRNA的互作，LncRNA與miRNA、mRNA、circRNA等相互的結(jié)合調(diào)控，目前各種數(shù)據(jù)庫大概有上百種，沒有系統(tǒng)性針對(duì)性的數(shù)據(jù)庫，以下是我們對(duì)數(shù)據(jù)的整理，通過數(shù)據(jù)庫查詢分類、數(shù)據(jù)庫功能及用途、示例結(jié)合分析、數(shù)據(jù)庫優(yōu)化等這四大項(xiàng)，進(jìn)行闡述和演示數(shù)據(jù)庫的查詢和使用，希望對(duì)您的實(shí)驗(yàn)項(xiàng)目有所幫助
1. 基因查詢數(shù)據(jù)庫：
查詢獲取你的基因信息及相關(guān)序列信息
①NCBI：https://www.ncbi.nlm.nih.gov/
②UCSC：http://genome.ucsc.edu/
③Ensembl：http://www.ensembl.org/index.html
④EBI：http ： //www.ebi.ac.uk/
⑤NIG：http： //www.nig.ac.jp/
MiRNA查詢數(shù)據(jù)庫：
①miRBase: http://www.mirbase.org
②microRNA.org:http://www.microrna.org/
③deepBase： http://deepbase.sysu.edu.cn/
④starBase： http://starbase.sysu.edu.cn/
⑤targetScan：http://www.targetscan.org/vert_70/
⑥TarBase: http://www.tarbase.com/
⑦miRanda： http://www.microrna.org/microrna/home.do
⑧RNAhybrid：https://bibiserv.cebitec.uni-bielefeld.de/
⑨CoGeMiR：http://cogemir.tigem.it/
⑩miRNApath：http://lgmb.fmrp.usp.br/mirnapath/tools.php
LncRNA查詢數(shù)據(jù)庫：
①Ensembl：http://www.ensembl.org/index.html
②LncRNAdb: http://www.lncrnadb.org/
③LNCipedia: https://lncipedia.org/
④CHIPbase: http://rna.sysu.edu.cn/chipbase/
⑤starBase： http://starbase.sysu.edu.cn/
circRNA查詢數(shù)據(jù)庫：
①circBase：http://www.circbase.org/
②CIRCpedia：http://www.picb.ac.cn/rnomics/circpedia/
③deepbase：http://rna.sysu.edu.cn/deepBase/
④starbase：http://starbase.sysu.edu.cn/index.php
常用數(shù)據(jù)庫功能用途介紹：
基因數(shù)據(jù)庫功能：
1. NCBI：
The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information
數(shù)據(jù)庫功能：
Submit：NCBI collects submissions of data for the world's largest public repository of biological and scientific information
Download：The majority of NCBI data are available for downloading, either directly from the NCBI FTP site or by using software tools to download custom datasets
Learn：NCBI creates a variety of educational products including courses, workshops, webinars, training materials and documentation. NCBI educational events are free and open to everyone. All NCBI educational materials are available for anyone to re-use and distribute.
Develop：NCBI provides a variety of resources that allow developers to access and manipulate NCBI data in their applications.
Analyze：NCBI provides a wide variety of data analysis tools that allow users to manipulate, align, visualize and evaluate biological data.
2. UCSC Genome Browser：
The UCSC Genome Browser is developed and maintained by the Genome Bioinformatics Group, a cross-departmental team within the UCSC Genomics Institute. the website has grown to include a broad collection of vertebrate and model organism assemblies and annotations, along with a large suite of tools for viewing, analyzing and downloading data.
數(shù)據(jù)庫功能：
Genome Browser：interactively visualize genomic data
BLAT：rapidly align sequences to the genome
Table Browser：download data from the Genome Browser database
Variant Annotation Integrator：get functional effect predictions for variant calls
Data Integrator：combine data sources from the Genome Browser database
Gene Sorter：find genes that are similar by expression and other metrics
Genome Browser in a Box (GBiB)：run the Genome Browser on your laptop or server
In-Silico PCR：rapidly align PCR primer pairs to the genome
LiftOver：convert genome coordinates between assemblies
VisiGene：interactively view in situ images of mouse and frog
MiRNA數(shù)據(jù)庫：
1. miRBase
the microRNA database
? The miRBase Registry provides miRNA gene hunters with unique names for novel miRNA genes prior to publication of results.
2. microRNA.org ：
Targets and Expression，Predicted microRNA targets & target downregulation scores. Experimentally observed expression patterns.
數(shù)據(jù)庫功能：
1. mirSVR predicted target site scoring method: Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites
2. microRNA target predictions: The microRNA.org resource: targets and expression.
3. miRanda application: Human MicroRNA targets.
4. miRanda algorithm: MicroRNA targets in Drosophila.
LncRNA數(shù)據(jù)庫：
1. Ensembl genome browser
Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species
數(shù)據(jù)庫功能：
Variant Effect Predictor
Gene expression in Ensembl
Retrieving sequences
Compare genes across species
SNPs and other variants for my gene
Use my own data in Ensembl
2. LncRNAab :
Long Noncoding RNA Database v2.0- The Reference Database For Functional Long Noncoding RNAs
circRNA數(shù)據(jù)庫：
1. circBase：
Circular RNA ( circ RNA) is a recent addition to the growing list of types of noncoding RNA．Here you can explore public circ RNA datasets and download the custom python scripts needed to dis cover cicRNAs in your own RNA-seq data
數(shù)據(jù)庫功能（Database function）
? Sequence-based search
? Search the database by identifier, gene description, genomic position, or their lists.
? Retrieve dataset slices by defining a set of conditions (table browser).
? Export tables in a variety of formats.
? Export FASTA files containing genomic sequence.
2. CIRCpedia：
CIRCpedia is an integrative database, aiming to annotating alternative back-splicing and alternative splicing in circRNAs across different cell lines. Through employing an upgraded circRNA characterization pipeline (CIRCexplorer2), thousands of alternative back-splicing and alternative splicing events in circRNAs were identified. All these identified alternative back-splicing and alternative splicing in circRNAs, together with novel exons, are formatted and classified for being easily searched, browsed and downloaded from CIRCpedia
基因查詢：以H19為例
UCSC數(shù)據(jù)庫
1. 打開主頁面
2. 點(diǎn)擊Genome Browser，選擇種屬，
3. 對(duì)話框中輸入基因，點(diǎn)擊“GO”
4. 即可查詢到基因的相關(guān)信息
數(shù)據(jù)庫優(yōu)化：
UCSC數(shù)據(jù)庫可查詢到基因的信息，以及該基因在不同物種中，序列的保守性等數(shù)據(jù)
2. miRNA查詢：
miRBase使用：以has-mir-9為例
1. 輸入網(wǎng)址，打開主頁面
2. “search by miRNA name or keyword’對(duì)話框中輸入miRNA名稱
3. 點(diǎn)擊“GO”查詢
4. 根據(jù)您的物種需要，點(diǎn)擊即可獲取該miRNA的相關(guān)信息
5. 點(diǎn)擊“Get sequence”，即可獲取序列信息
數(shù)據(jù)庫優(yōu)化：
MiRbase是一款非常強(qiáng)大的miRNA查詢數(shù)據(jù)庫，可查詢miRNA相關(guān)信息外，還可以做與mRNA的結(jié)合預(yù)測分析，詳細(xì)請您進(jìn)一步探知
LncRNA查詢：以LncRNA H19為例
Ensembl genome browser數(shù)據(jù)庫：
1. 打開主頁面
2. 選取種屬，對(duì)話框輸入查詢LncRNA
3. 點(diǎn)擊進(jìn)入，即可獲取LncRNAH19的相關(guān)信息
數(shù)據(jù)庫優(yōu)化：Ensembl數(shù)據(jù)庫是一款可查詢LncRNA不同剪接變體及詳細(xì)信息的數(shù)據(jù)庫，對(duì)于LncRNA有多種剪接變體來說，可查詢獲取得到確切的研究變體序列
CircRNA查詢：
CircRNA數(shù)據(jù)庫：以CDR1（小腦變性相關(guān)蛋白1）為例，查詢環(huán)狀RNA信息
數(shù)據(jù)庫優(yōu)化：circbase可查詢基因轉(zhuǎn)錄對(duì)應(yīng)的環(huán)狀RNA信息外，還可以直接通過輸入環(huán)狀RNA的ID或是名稱進(jìn)行查詢，可得到詳細(xì)的環(huán)狀RNA的信息