Author： 苗奔奔 HiPlot (https://hiplot.com.cn)生物信息学分析云平台开发者
Courses: https://www.bilibili.com/video/BV1Ey4y1i7Q7?spm_id_from=333.999.0.0
Github: https://github.com/benben-miao/Bioinformatics-Servers
WeChat: https://mp.weixin.qq.com/s/jFqwIuKQ4ihyoTLnBi0fMw
1. 基因水平
1.1 近缘物种序列比对:
NCBI-Blast: https://blast.ncbi.nlm.nih.gov/Blast.cgi
EMBL-Blast: https://www.ebi.ac.uk/Tools/sss/ncbiblast/nucleotide.html
1.2 多序列比对
Clustal Omega: https://www.ebi.ac.uk/Tools/msa/clustalo/
MAFFT: https://www.ebi.ac.uk/Tools/msa/mafft/
1.3 序列可视化
Seq2Logo: https://services.healthtech.dtu.dk/service.php?Seq2Logo-2.0
Blast2Logo: https://services.healthtech.dtu.dk/service.php?Blast2logo-1.1
1.4 进化树构建
MEGA: https://megasoftware.net
Clustal Omega: https://www.ebi.ac.uk/Tools/msa/clustalo/
1.5 DNA分子质量和碱基组成
BioEdit: https://www.bioedit.com
1.6 DNA序列酶切位点和翻译
BioEdit: https://www.bioedit.com
1.7 基因启动子顺式作用元件
Promoter: https://services.healthtech.dtu.dk/service.php?Promoter-2.0
Softberry: http://linux1.softberry.com
PlantCARE: http://bioinformatics.psb.ugent.be/webtools/plantcare/html
Plant: https://www.dna.affrc.go.jp/PLACE/?action=newplace
TransFac: http://gene-regulation.com/
JASPAR: https://jaspar.genereg.net/
EPD: https://epd.epfl.ch/index.php
顺式cis、反式trans、增强子enhancer、终止子terminator、沉默子silencer、绝缘子insulator、专一性元件是一类能被特定转录因子识别和结合 , 调控基因专一性表达的 DNA 序列，如热激应答元件，激素应答元件，cAMP应答元件，金属应答元件。
1.8 翻译起始位点
NetStart: https://services.healthtech.dtu.dk/service.php?NetStart-1.0
1.9 基因在染色体上定位
GSDS: http://gsds.cbi.pku.edu.cn
1.10 基因在组织和发育阶段的表达记录
BGEE: https://bgee.org
2. 蛋白质水平
2.1 蛋白质开放阅读框预测
NCBI ORF: http://www.ncbi.nlm.nih.gov/projects/gorf/orfig.cgi
2.2 蛋白质理化性质
ProtScale: https://web.expasy.org/protscale/
参数选择 Amino acid scale：Hphob. / Kyte & Doolittle；Window size：19, (负：亲水，正：疏水)
ProtParam: https://web.expasy.org/protparam/
氨基酸数目、分子量（Da 道尔顿）、等电点（酸性：<7，碱性：>7）、不稳定指数（40）、亲水性（正：亲水，负：疏水）
2.3 蛋白质氨基酸成分
PredictkProtein: https://www.predictprotein.org/
2.4 蛋白质保守功能结构域
NCBI CDD: https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi
SMART: http://smart.embl-heidelberg.de
ProSite: https://prosite.expasy.org/
PFam: http://pfam.xfam.org/search/sequence
HMMER: https://www.ebi.ac.uk/Tools/hmmer/
2.5 蛋白质保守基序分析
MEME: http://meme-suite.org/
2.6 蛋白质二级结构预测
NPSA SOPMA: https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_sopma.html
PSI Pred: http://bioinf.cs.ucl.ac.uk/psipred/#
α-螺旋 Alpha helix、β-折叠 Beta turn、无规则卷曲Random coil 、延伸链Extended strand
2.7 蛋白质三级结构分析
Swiss-Model: https://swissmodel.expasy.org/
Robetta: http://robetta.bakerlab.org/
CPHmodels: http://www.cbs.dtu.dk/services/CPHmodels
Phyre2: http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index
2.8 蛋白质模型预测
SwissModel: https://swissmodel.expasy.org
2.9 蛋白质相似性预测
MSD: https://www.ebi.ac.uk/msd-srv/ssm/
2.10 蛋白质磷酸化位点分析
NetPhos: https://services.healthtech.dtu.dk/service.php?NetPhos-3.1
2.11 蛋白质N-糖基化位点分析
NetNGlyc: https://services.healthtech.dtu.dk/service.php?NetNGlyc-1.0
2.12 蛋白质O-糖基化位点分析
YinOYang: https://services.healthtech.dtu.dk/service.php?YinOYang-1.2
2.13 蛋白质二硫键预测分析
SCRATCH: http://www.ics.uci.edu/~baldig/scratch/index.html
2.14 蛋白质亚细胞定位
ProteinAtlas: http://www.proteinatlas.org/ENSG00000186350-RXRA/cell
GeneCards: https://www.genecards.org
ProteinAtlas: https://www.proteinatlas.org
TargetP: https://services.healthtech.dtu.dk/service.php?TargetP-2.0
PSORT: https://www.genscript.com/psort.html
PSORT: http://psort1.hgc.jp/form.html
Plant: http://wolfpsort.org
亚细胞-细胞器：细胞膜、细胞骨架、细胞质、线粒体、叶绿体、内质网、过氧化物酶体、细胞核
2.15 蛋白质核定位序列预测
NLStradamus: http://www.moseslab.csb.utoronto.ca/NLStradamus/
2.16 蛋白质的跨膜结构域预测
DeepTMHMM: https://dtu.biolib.com/app/DeepTMHMM/run
TMHMM: https://services.healthtech.dtu.dk/service.php?TMHMM-2.0
TMpred: http://www.ch.embnet.org/software/TMPRED_form.html
SOSUI: http://harrier.nagahama-i-bio.ac.jp/sosui/sosui_submit.html
2.17 蛋白质的信号肽预测
SignalP: https://services.healthtech.dtu.dk/service.php?SignalP-5.0
2.18 蛋白质网络互作
StringDB: https://string-db.org
2.19 GO和KEGG注释
GO: http://geneontology.org
KEGG: https://www.genome.jp/kegg/
KEGG: https://www.kegg.jp
BlastKOALA: https://www.kegg.jp/blastkoala/
GhostKOALA: https://www.kegg.jp/ghostkoala/
KofamKOALA: https://www.genome.jp/tools/kofamkoala/
DAVID: https://david.ncifcrf.gov
KOBAS: http://kobas.cbi.pku.edu.cn
G-Profile: https://biit.cs.ut.ee/gprofiler/gost
Enrichr: https://maayanlab.cloud/Enrichr/
MetaScape: http://metascape.org/gp/index.html#/main/step1
FunRich: http://funrich.org/
3. 转录因子水平
3.1 TF基于蛋白质序列预测
GuoLab: http://bioinfo.life.hust.edu.cn/guo_lab#!/
Plant TFDB:http://planttfdb.gao-lab.org/
Animal TFDB: http://bioinfo.life.hust.edu.cn/AnimalTFDB/#!/
Human TFDB: http://bioinfo.life.hust.edu.cn/HumanTFDB#!/
3.2 TF靶基因结合位点预测
Animal: http://bioinfo.life.hust.edu.cn/AnimalTFDB/#!/tfbs_predict
HOCOMOCO: https://hocomoco11.autosome.ru
JASPAR: https://jaspar.genereg.net
FootPrintDB: http://floresta.eead.csic.es/footprintdb/?search
3.3 TF Motif 可视化
DRV: https://drv.brc.hu/
TFBSShape: https://tfbsshape.usc.edu
WebLogo: http://weblogo.threeplusone.com
3.4 TF靶基因预测
HTFtarget: http://bioinfo.life.hust.edu.cn/hTFtarget#!/
JASPAR: https://jaspar.genereg.net
TRRUST: https://www.grnpedia.org/trrust/
ChipBase: https://rna.sysu.edu.cn/chipbase/index.php
CistromeDB: http://cistrome.org/db/#/
CancerTarget: http://cistrome.org/CistromeCancer/CancerTarget/
TCGAEnhancer: http://cistrome.org/CistromeCancer/TCGA_enhancer/
TransFac: https://new.bio-store.org/#
GenexPlain: https://platform.genexplain.com/bioumlweb/#
HOMER: http://homer.ucsd.edu/homer/motif/
KnockTF: http://www.licpathway.net/KnockTF/index.html
3.5 TF DBD预测(DNA-binding Domain)
TF DBD: https://transcriptionfactor.org
3.6 TF靶基因启动子、增强子
Promoter: https://services.healthtech.dtu.dk/service.php?Promoter-2.0
GTRD: http://gtrd.biouml.org/#!
TF蛋白质转录调控域(Transcription Regulation Domain)
TF蛋白质寡聚化位点(Oligomerization Site)
TF蛋白质核定位信号(Nuclear Location Signal，NLS)