生物数据库与在线工具

生物数据库

      生物数据库是收集自科学实验、出版文献、高通量实验技术和计算分析等生命科学信息库，它包含来自基因组学、蛋白质组学、代谢组学、微阵列基因表达和系统发育学等领域的信息。

      生物数据库大致可分为序列、结构和功能数据库。序列数据库储存核酸和蛋白质序列；结构数据库储存RNA和蛋白质的结构信息；功能数据库提供关于基因产物的生理作用信息（例如，酶活性、突变表型和生物途径等）。

数据库类型

    生物数据库有两个常见的概念：一级数据库和二级数据库。一级数据库储存实验中获得数据；二级数据库使用其它数据库（例如，一级数据库）作为其信息源，然后根据需要进行处理或分析获得的结果。

 

数据库查找

       查找生物数据库的重要资源是NAR（Nucleic Acids Research，核酸研究）期刊的特刊，它将许多与生物学和生物信息学相关的公开在线数据库分类，截止2018年共收录了1737个数据库。

    NAR将所有数据库划分为15类，核苷酸序列数据库、RNA序列数据库、蛋白质序列数据库、结构数据库、基因组学数据库（非脊椎动物）、代谢和信号通路数据库、人类和其他脊椎动物基因组数据库、人类基因和疾病数据库、微阵列数据和其他基因表达数据库、蛋白质组学资源数据库、其他分子生物学数据库、细胞器数据库、植物数据库、免疫学数据库和细胞生物学数据库。

 

在线工具

      NAR除了收录生物数据库，每年还发布可用于分子生物学数据分析和可视化的网络资源。

 

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

The 2018 Nucleic Acids Research database issue and the online molecular biology database collection

Editorial: The 15th annual Nucleic Acids Research web server issue 2017

Editorial: The 16th annual Nucleic Acids Research web server issue 2018