生物数据库与在线工具

生物数据库

生物数据库基于科学实验数据、出版文献资料以及高通量实验技术和计算分析方法构建了生命科学研究信息资源库。该数据库系统涵盖了基因组学（Genome Analysis）、蛋白质组学（Protein Analysis）、代谢组学（Metabolomics）、微阵列基因表达分析（Microarray Gene Expression）和系统发育学（Systematics and Developmental Biology）等多个研究领域的核心数据与分析结果。

生物数据库主要可分为三个类别：序列、结构与功能数据库。其中序列数据库专门存储核酸碱基序列与蛋白质氨基酸序列；而结构数据库则记录了RNA分子与蛋白质的三维构象信息；此外，在功能数据库中，则详细记录了基因产物的各种生理作用机制及其相关数据（例如：酶催化作用的具体步骤；基因突变对产物功能的影响；以及基因调控通路的具体表现形式等）。

数据库类型

生物 database有两种常见的类别: 一级 database 和二级 database. 一级 database 用于存储实验中获得的数据; 二级 database 以其他 (如一级) 数据库的信息为基础, 并根据具体需求进行处理或分析以获取结果.

数据库查找

获取生物数据库的关键来源是《核酸研究》（NAR：Nucleic Acids Research）期刊中的专题综述部分；该期刊系统地整理了与生物科学及生物信息学领域相关的网络数据库，并在2018年底统计显示共有1737个数据库被收录。

NAR系统将15种类型的生物信息学数据系统性地划分为15个类别以便于研究者进行跨学科分析。（非-脊椎动物）生命科学领域的研究者普遍采用这一分类方法以提高研究效率与数据整合能力

在线工具

NAR除了收集生物数据库之外，并非仅此用途，在线发表内容还包括每年还会发布用于分子生物学数据分析和可视化展示的网络资源

表1 2017年网络资源

Web Server name	URL	Brief description
agriGO v2	http://systemsbiology.cau.edu.cn/agriGOv2/	GO analysis for agricultural species
AMMOS2	http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php	Energy minimization of protein–ligand complexes
antiSMASH	http://antismash.secondarymetabolites.org/	Secondary metabolite biosynthetic gene cluster mining in bacterial and fungal genomes
ARTS	http://arts.ziemertlab.com	Biosynthetic gene cluster mining for novel antibiotics
BAR 3.0	http://bar.biocomp.unibo.it/bar3	Protein structure and function annotation
BepiPred-2.0	http://www.cbs.dtu.dk/services/BepiPred-2.0/	B-cell epitope prediction from a protein sequence
BioAtlas	http://bioatlas.compbio.sdu.dk	Visualization of microbiome and metagenome locations
BIS2Analyzer	http://www.lcqb.upmc.fr/BIS2Analyzer/	Analysis of coevolving amino-acid pairs in protein sequences
BusyBee	https://ccb-microbe.cs.uni-saarland.de/busybee	Metagenome binning
CAFE	https://github.com/younglululu/CAFE	Stand-alone program for alignment-free comparison of metagenome data
Cancer PanorOmics	http://panoromics.irbbarcelona.org	Mapping of cancer mutations to 3D protein–protein interaction sites
COFACTOR	http://zhanglab.ccmb.med.umich.edu/COFACTOR/	Structure-based protein function annotation
compleXView	http://xvis.genzentrum.lmu.de/compleXView	Protein-protein interaction based on affinity purification mass spectrometry
ConTra v3	http://bioit2.irc.ugent.be/contra/v3	Transcription factor binding sites analysis
CPC2	http://cpc2.cbi.pku.edu.cn	Protein coding potential of RNA transcripts
CSPADE	http://cspade.fimm.fi/	Chemoinformatics bioactivity assay visualization
CSTEA	http://comp-sysbio.org/cstea/	Analysis of time-series gene expression data on cell state transitions
DEOGEN2	http://deogen2.mutaframe.com/	Prediction of deleterious mutations in proteins
DNAproDB	http://dnaprodb.usc.edu	Structural analysis of DNA–protein complexes
DSSR	http://jmol.x3dna.org	DNA and RNA structure visualization
DynOmics	http://dyn.life.nthu.edu.tw/oENM/	Protein molecular dynamics using elastic network models
EBISearch	http://www.ebi.ac.uk/ebisearch	Web services text search in EMBL-EBI data
FireProt	http://loschmidt.chemi.muni.cz/fireprot	Design of thermostable proteins
GalaxyHomomer	http://galaxy.seoklab.org/cgi-bin/submit.cgi?type=HOMOMER	Prediction of protein homo-oligomer structure
GASS-WEB	http://gass.unifei.edu.br/	Identification of enzyme active sites
GeMSTONE	http://gemstone.yulab.org/	Genetic variant prioritization in human disease
Gene ORGANizer	http://geneorganizer.huji.ac.il	Linkage of human genes to their affected body organs
GenProBiS	http://genprobis.insilab.org	Mapping of SNPs to protein binding sites
GEPIA	http://gepia.cancer-pku.cn/	Analysis of differential gene expression in cancer
GeSeq	https://chlorobox.mpimp-golm.mpg.de/geseq.html	Annotation of chloroplast genomes
GibbsCluster	http://www.cbs.dtu.dk/services/GibbsCluster-2.0	Detection of protein short linear motifs
GPCR-SSFE 2.0	http://www.ssfa-7tmr.de/ssfe2/	Homology modeling of G-protein coupled receptors
GWAB	http://www.inetbio.org/gwab/	Network-based genome wide association analysis
HDOCK	http://hdock.phys.hust.edu.cn/	Protein–protein and protein–DNA/RNA docking
HGVA	http://bioinfodev.hpc.cam.ac.uk/web-apps/hgva	Archive of human genetic variant annotations
HH-MOTiF	http://chimborazo.biochem.mpg.de/	Detection of protein short linear motifs
I-TASSER-MR	http://zhanglab.ccmb.med.umich.edu/I-TASSER-MR/	Protein structure modeling for X-ray crystallography
INTAA	http://bioinfo.uochb.cas.cz/INTAA/	Analysis of amino acid interaction energies
IntaRNA 2.0	http://rna.informatik.uni-freiburg.de/IntaRNA/Input.jsp	Prediction of interactions between RNA molecules
IslandViewer 4.0	http://www.pathogenomics.sfu.ca/islandviewer4/	Prediction of bacterial genomic islands (horizontal gene transfer)
kpLogo	http://kplogo.wi.mit.edu/	Detection and visualization of short sequence motifs
LigParGen	http://jorgensenresearch.com/ligpargen	Force field parameters for molecular dynamics
LimTox	http://limtox.bioinfo.cnio.es	Text mining for compound toxicity
mCSM-NA	http://structure.bioc.cam.ac.uk/mcsm_na	Prediction of protein mutation effect on nucleic acid binding affinity
MicrobiomeAnalyst	http://microbiomeanalyst.ca	Analysis of microbiome data
MinePath	http://www.minepath.org	Differential expression analysis for regulatory network subpaths
ModFOLD6	http://www.reading.ac.uk/bioinf/ModFOLD/	Protein structure quality assessment
mTCTScan	http://jjwanglab.org/mTCTScan	Mutation prioritization for cancer drug response
MutaGene	https://www.ncbi.nlm.nih.gov/projects/mutagene/	Visualization and analysis of mutational profiles in cancer
NNAlign-2.0	http://www.cbs.dtu.dk/services/NNAlign-2.0	Detection of ligand motifs for receptor–ligand interactions
NOREVA	http://server.idrb.cqu.edu.cn/noreva/	Evaluation of data normalization methods for mass spectrometry based metabolomics data
Olelo	http://www.hpi.de/plattner/olelo	Text mining in PubMed
OmicSeq	http://www.omicseq.org	Search for omics data in major repositories
P4P	http://sing.ei.uvigo.es/p4p	Bacterial strain classification based on peptide datasets
Pathview	http://pathview.uncc.edu/	Visualization and annotation of metabolic pathways
pepATTRACT	http://bioserv.rpbs.univ-paris-diderot.fr/services/pepATTRACT	Prediction of protein–peptide docking
PharmMapper	http://lilab.ecust.edu.cn/pharmmapper	Drug target search using pharmacophore mapping
PhD-SNPg	http://snps.biofold.org/phd-snpg	Deleterious SNP classification
PIGSPro	http://cassandra.med.uniroma1.it/AbPrediction/web/pigs.php	Modeling of immunoglobulin variable domains
plantiSMASH	http://plantismash.secondarymetabolites.org	Detection of biosynthetic gene clusters in plants
PMut	http://mmb.irbbarcelona.org/PMut/	Prediction of disease potential for protein mutations
Prism3	http://prism3.magarveylab.ca/prism	Prediction of natural product structures from biosynthetic gene clusters
ProteinsAPI	http://www.ebi.ac.uk/proteins/api	Web service for protein data from UniProtKB
ProteinsPlus	http://proteins.plus	Structure-based modeling of proteins
ProteoSign	http://bioinformatics.med.uoc.gr/ProteoSign	Protein differential abundance analysis
ReFOLD	http://www.reading.ac.uk/bioinf/ReFOLD/	Protein structure refinement
RegulatorTrail	https://regulatortrail.bioinf.uni-sb.de	Analysis of transcription factors and target genes
RiPPMiner	http://www.nii.ac.in/rippminer.html	Prediction of chemical structures for ribosomally synthesized and post translationally modified peptides
RNA workbench	https://github.com/bgruening/galaxy-rna-workbench	Stand-alone collection of tools for analyzing RNAseq and RNA sequence data
RNA-MoIP	http://rnamoip.cs.mcgill.ca/	Prediction of RNA 2D and 3D structure
SBSPKSv2	http://www.nii.ac.in/sbspks2.html	Analysis of polyketide synthases
SCENERY	http://mensxmachina.org/en/software/	Network reconstruction from cytometry data
SDM	http://structure.bioc.cam.ac.uk/sdm2	Prediction of stability in protein mutants
SeMPI	http://www.pharmaceutical-bioinformatics.de/sempi/	Prediction of polyketide synthase products from biosynthetic gene clusters
SLiMSearch	http://slim.ucd.ie/slimsearch/	Detection of protein short linear motifs
SODA	http://protein.bio.unipd.it/soda/	Prediction of solubility in protein mutants
SpartaABC	http://spartaabc.tau.ac.il/webserver	Sequence simulation with indels
ThreaDomEx	http://zhanglab.ccmb.med.umich.edu/ThreaDomEx	Prediction of protein domains and domain boundaries
Tools at EMBL-EBI	http://www.ebi.ac.uk/Tools/webservices/	Web service tools from EMBL-EBI
TraitRateProp	http://traitrate.tau.ac.il/prop	Test of sequence evolution association with phenotype
TRAPP	http://trapp.h-its.org	Analysis of protein binding site dynamics
VCF.Filter	https://biomedical-sequencing.at/VCFFilter/	Stand-alone program for filtering and annotating genetic variants in vcf files
Web3DMol	http://web3dmol.duapp.com/	Protein structure visualization
WebGestalt	http://www.webgestalt.org	Gene set functional enrichment analysis
WoPPER	http://WoPPER.ba.itb.cnr.it/	Detection of bacterial genome regions with coordinated gene expression changes
XSuLT	http://structure.bioc.cam.ac.uk/xsult	Annotation and visualization of protein multiple sequence alignment

表2 2018年网络资源

Web server name	URL	Brief description
AAI-profiler	http://ekhidna2.biocenter.helsinki.fi/AAI	proteome average amino acid identity comparison
AlloFinder	http://mdl.shsmu.edu.cn/ALF/	allosteric modulator identification
ArDock	http://ardock.ibcp.fr	protein–protein interaction region prediction
BAGEL4	http://bagel4.molgenrug.nl	secondary metabolite gene clusters (RIPPs, bacteriocins)
BaMM	https://bammmotif.mpibpc.mpg.de	nucleotide binding motifs
BeStSel	http://bestsel.elte.hu	circular dichroism spectroscopy based protein secondary structure analysis
BRepertoire	http://mabra.biomed.kcl.ac.uk/BRepertoire	antibody repertoire analysis
BUSCA	http://busca.biocomp.unibo.it	protein subcellular localization prediction
CABS-flex 2.0	http://biocomp.chem.uw.edu.pl/CABSflex2	simulation of protein structure flexibility
CalFitter	https://loschmidt.chemi.muni.cz/calfitter/	protein thermal denaturation analysis
CASTp 3.0	http://sts.bioe.uic.edu/castp/	topology of protein pockets, cavities and channels
CavityPlus	http://www.pkumdl.cn/cavityplus	protein binding site cavities
CellAtlasSearch	http://www.cellatlassearch.com	single cell gene expression data search
cgDNAweb	http://cgDNAweb.epfl.ch	double-stranded DNA coarse-grain models
CircadiOmics	http://circadiomics.ics.uci.edu	circadian rhythm dataset analysis and repository
COACH-D	http://yanglab.nankai.edu.cn/COACH-D/	protein–ligand binding site prediction
Coloc-stats	https://hyperbrowser.uio.no/coloc-stats/	genomic location enrichment analysis
ComplexContact	http://raptorx2.uchicago.edu/ComplexContact/	protein heterodimer complex residue–residue contact prediction
CoNekT-Plants	http://conekt.plant.tools	comparative analyses of plant gene co-expression
CRISPOR	http://crispor.org	guide sequences for CRISPR/Cas9 genome editing
CRISPRCasFinder	https://crisprcas.i2bc.paris-saclay.fr	CRISPR array and Cas gene detection
CSAR-web	http://genome.cs.nthu.edu.tw/CSAR-web	contig scaffolding
dbCAN2	http://cys.bios.niu.edu/dbCAN2	carbohydrate-active enzyme annotation
DynaMut	http://biosig.unimelb.edu.au/dynamut/	point mutation effects on protein stability and dynamics
easyFRAP-web	https://easyfrap.vmnet.upatras.gr/	protein mobility analysis with fluorescence recovery after photobleaching data
EviNet	https://www.evinet.org/	gene set network enrichment analysis
ezTag	http://eztag.bioqrator.org	biomedical concept annotation
FragFit	http://proteinformatics.de/FragFit	protein segment modeling of cryo-EM density maps
Freiburg RNA tools	http://rna.informatik.uni-freiburg.de	RNA analysis
GADGET	http://gadget.biosci.gatech.edu	population-based distributions of genetic variants
Galaxy	https://usegalaxy.org	biomedical data analysis workflows
Galaxy HiCExplorer	https://hicexplorer.usegalaxy.eu	chromatin 3D conformation analysis
GDA	http://gda.unimore.it/	integration of drug response, gene expression profiles and mutations for cancer
GeneMANIA	http://genemania.org	gene function prediction
geno2pheno[ngs-freq]	http://ngs.geno2pheno.org	viral drug resistance prediction
GIANT 2.0	http://giant-v2.princeton.edu	human tissue-specific gene functional relationships
GPCRM	http://gpcrm.biomodellab.eu/	G protein-coupled receptors structure modeling
gRINN	http://grinn.readthedocs.io	protein molecular dynamics residue interaction energies
GWAS4D	http://mulinlab.org/gwas4d	prioritization of regulatory variants from GWAS data
HMMER	http://www.ebi.ac.uk/Tools/hmmer	profile hidden Markov models homology search
HotSpot Wizard 3.0	http://loschmidt.chemi.muni.cz/hotspotwizard3	protein engineering directed mutation
HPEPDOCK	http://huanglab.phys.hust.edu.cn/hpepdock/	peptide–protein docking
HSYMDOCK	http://huanglab.phys.hust.edu.cn/hsymdock/	symmetric protein complex docking
InterEvDock2	http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock2/	protein–protein docking
INTERSPIA	http://bioinfo.konkuk.ac.kr/INTERSPIA/	protein–protein interactions in multiple species
iPath3.0	http://pathways.embl.de	metabolic pathway visualization and customization
IUPred2A	http://iupred2a.elte.hu	intrinsically disordered protein regions
Kinact	http://biosig.unimelb.edu.au/kinact/	kinase activating missense mutations prediction
KnotGenome	http://knotgenom.cent.uw.edu.pl/	topological analysis of chromosome knots and links
LitVar	https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/LitVar	genetic variant information retrieval from PubMed
LOLAweb	http://lolaweb.databio.org	genomic region enrichment analysis
MetaboAnalyst 4.0	http://metaboanalyst.ca	metabolomics data analysis
MetExplore	https://metexplore.toulouse.inra.fr/metexplore2/	metabolic network analysis
MiGA	http://microbial-genomes.org/	prokaryotic genome and metagenome classification
MISTIC2	https://mistic2.leloir.org.ar	residue pair covariation in protein families
MOLEonline	https://mole.upol.cz	biomolecule channels, tunnels, and pores
mTM-align	http://yanglab.nankai.edu.cn/mTM-align/	protein structure multiple alignment and database search
Mutalisk	http://mutalisk.org	somatic mutations correlation with genomic, transcriptional and epigenomic features
Ocean Gene Atlas	http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/	marine plankton gene geolocation and abundance
oli2go	http://oli2go.ait.ac.at/	PCR primer and hybridization probe design for non-human DNA
OmicsNet	http://www.omicsnet.ca	molecular interactions networks visualization
oriTfinder	http://bioinfo-mml.sjtu.edu.cn/oriTfinder	origin of transfer sites in bacterial mobile genetic elements
PaintOmics 3	http://bioinfo.cipf.es/paintomics/	visualization of omics data on KEGG pathways
PANNZER2	http://ekhidna2.biocenter.helsinki.fi/sanspanz/	protein function prediction
PatScanUI	https://patscan.secondarymetabolites.org/	DNA and protein sequence pattern search
PhytoNet	http://www.gene2function.de	phytoplankton gene expression profiles
pirScan	http://cosbi4.ee.ncku.edu.tw/pirScan/	piRNA target prediction
ProTox-II	http://tox.charite.de/protox_II	chemical toxicity prediction
psRNATarget	http://plantgrn.noble.org/psRNATarget/	plant small RNA target prediction
PSSMSearch	http://slim.ucd.ie/pssmsearch/	protein motifs for binding and post-translational modification
PUG-REST	https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest	PubChem cheminformatics programmatic access
RepeatsDB-lite	http://protein.bio.unipd.it/repeatsdb-lite	tandem repeats in proteins
RNApdbee 2.0	http://lepus.cs.put.poznan.pl/rnapdbee-2.0/	RNA secondary structure annotation
RSAT	http://www.rsat.eu/	DNA regulatory motifs
SMARTIV	http://smartiv.technion.ac.il/	RNA sequence and structure motifs for RNA binding proteins
SNPnexus	http://www.snp-nexus.org	SNP functional annotation
SPAR	https://www.lisanwanglab.org/SPAR	analysis of small RNA sequencing data
SWISS-MODEL	https://swissmodel.expasy.org	structure homology modeling for proteins and protein complexes
TAM 2.0	http://www.scse.hebut.edu.cn/tam/	microRNA set enrichment analysis
TCRmodel	http://tcrmodel.ibbr.umd.edu/	T cell receptor structure modeling
UNRES	http://unres-server.chem.ug.edu.pl	coarse-grained simulation of protein structure
VarAFT	http://varaft.eu	disease-causing variants annotation
WEGO 2.0	http://wego.genomics.org.cn	Gene Ontology visualization
X2K Web	http://X2K.cloud	kinase enrichment analysis for differentially expressed gene signatures
xiSPEC	http://spectrumviewer.org	proteomics mass spectrometry data analysis

参考资料

https://en.wikipedia.org/wiki/Biological_database

Year 2018's Yearly Issue of the Nucleic Acids Research Database and the Molecular Biology Database Repository (%20https://doi.org/10.1093/nar/gkx1235)

The special section of the 15th edition of the Nucleic Acid Research online journal, issue number 2017, presents a comprehensive collection of articles dedicated to advancing the field of nucleic acids research.

The 16th anniversary edition of the Nucleic Acid Research web server in 2018.

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