Author： 苗奔奔 HiPlot (https://hiplot.com.cn)生物信息學(xué)分析云平臺開發(fā)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 近緣物種序列比對:
NCBI-Blast: https://blast.ncbi.nlm.nih.gov/Blast.cgi
EMBL-Blast: https://www.ebi.ac.uk/Tools/sss/ncbiblast/nucleotide.html
1.2 多序列比對
Clustal Omega: https://www.ebi.ac.uk/Tools/msa/clustalo/
MAFFT: https://www.ebi.ac.uk/Tools/msa/mafft/
1.3 序列可視化
Seq2Logo: https://services.healthtech.dtu.dk/service.php?Seq2Logo-2.0
Blast2Logo: https://services.healthtech.dtu.dk/service.php?Blast2logo-1.1
1.4 進(jìn)化樹構(gòu)建
MEGA: https://megasoftware.net
Clustal Omega: https://www.ebi.ac.uk/Tools/msa/clustalo/
1.5 DNA分子質(zhì)量和堿基組成
BioEdit: https://www.bioedit.com
1.6 DNA序列酶切位點(diǎn)和翻譯
BioEdit: https://www.bioedit.com
1.7 基因啟動子順式作用元件
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
順式cis、反式trans、增強(qiáng)子enhancer、終止子terminator、沉默子silencer、絕緣子insulator、專一性元件是一類能被特定轉(zhuǎn)錄因子識別和結(jié)合 , 調(diào)控基因?qū)Ｒ恍员磉_(dá)的 DNA 序列，如熱激應(yīng)答元件，激素應(yīng)答元件，cAMP應(yīng)答元件，金屬應(yīng)答元件。
1.8 翻譯起始位點(diǎn)
NetStart: https://services.healthtech.dtu.dk/service.php?NetStart-1.0
1.9 基因在染色體上定位
GSDS: http://gsds.cbi.pku.edu.cn
1.10 基因在組織和發(fā)育階段的表達(dá)記錄
BGEE: https://bgee.org
2. 蛋白質(zhì)水平
2.1 蛋白質(zhì)開放閱讀框預(yù)測
NCBI ORF: http://www.ncbi.nlm.nih.gov/projects/gorf/orfig.cgi
2.2 蛋白質(zhì)理化性質(zhì)
ProtScale: https://web.expasy.org/protscale/
參數(shù)選擇 Amino acid scale：Hphob. / Kyte & Doolittle；Window size：19, (負(fù)：親水，正：疏水)
ProtParam: https://web.expasy.org/protparam/<br />氨基酸數(shù)目、分子量（Da 道爾頓）、等電點(diǎn)（酸性：<7，堿性：>7）、不穩(wěn)定指數(shù)（40）、親水性（正：親水，負(fù)：疏水）
2.3 蛋白質(zhì)氨基酸成分
PredictkProtein: https://www.predictprotein.org/
2.4 蛋白質(zhì)保守功能結(jié)構(gòu)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 蛋白質(zhì)保守基序分析
MEME: http://meme-suite.org/
2.6 蛋白質(zhì)二級結(jié)構(gòu)預(yù)測
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-折疊 Beta turn、無規(guī)則卷曲Random coil 、延伸鏈Extended strand
2.7 蛋白質(zhì)三級結(jié)構(gòu)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 蛋白質(zhì)模型預(yù)測
SwissModel: https://swissmodel.expasy.org
2.9 蛋白質(zhì)相似性預(yù)測
MSD: https://www.ebi.ac.uk/msd-srv/ssm/
2.10 蛋白質(zhì)磷酸化位點(diǎn)分析
NetPhos: https://services.healthtech.dtu.dk/service.php?NetPhos-3.1
2.11 蛋白質(zhì)N-糖基化位點(diǎn)分析
NetNGlyc: https://services.healthtech.dtu.dk/service.php?NetNGlyc-1.0
2.12 蛋白質(zhì)O-糖基化位點(diǎn)分析
YinOYang: https://services.healthtech.dtu.dk/service.php?YinOYang-1.2
2.13 蛋白質(zhì)二硫鍵預(yù)測分析
SCRATCH: http://www.ics.uci.edu/~baldig/scratch/index.html
2.14 蛋白質(zhì)亞細(xì)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
亞細(xì)胞-細(xì)胞器：細(xì)胞膜、細(xì)胞骨架、細(xì)胞質(zhì)、線粒體、葉綠體、內(nèi)質(zhì)網(wǎng)、過氧化物酶體、細(xì)胞核
2.15 蛋白質(zhì)核定位序列預(yù)測
NLStradamus: http://www.moseslab.csb.utoronto.ca/NLStradamus/
2.16 蛋白質(zhì)的跨膜結(jié)構(gòu)域預(yù)測
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 蛋白質(zhì)的信號肽預(yù)測
SignalP: https://services.healthtech.dtu.dk/service.php?SignalP-5.0
2.18 蛋白質(zhì)網(wǎng)絡(luò)互作
StringDB: https://string-db.org
2.19 GO和KEGG注釋
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. 轉(zhuǎn)錄因子水平
3.1 TF基于蛋白質(zhì)序列預(yù)測
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靶基因結(jié)合位點(diǎn)預(yù)測
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 可視化
DRV: https://drv.brc.hu/
TFBSShape: https://tfbsshape.usc.edu
WebLogo: http://weblogo.threeplusone.com
3.4 TF靶基因預(yù)測
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預(yù)測(DNA-binding Domain)
TF DBD: https://transcriptionfactor.org
3.6 TF靶基因啟動子、增強(qiáng)子
Promoter: https://services.healthtech.dtu.dk/service.php?Promoter-2.0
GTRD: http://gtrd.biouml.org/#!
TF蛋白質(zhì)轉(zhuǎn)錄調(diào)控域(Transcription Regulation Domain)
TF蛋白質(zhì)寡聚化位點(diǎn)(Oligomerization Site)
TF蛋白質(zhì)核定位信號(Nuclear Location Signal，NLS)
