生物学(Biology)

生物信息(Bioinfomatics)

中国医学科学院医学信息研究所：https://www.imicams.ac.cn/

NCBI: https://www.ncbi.nlm.nih.gov/

https://www.ncbi.nlm.nih.gov/projects/faspftp/

https://www.ncbi.nlm.nih.gov/home/learn/

生信菜鸟团: http://www.bio-info-trainee.com/

PLOB： https://www.plob.org/

bioengx：http://www.bioengx.com/

biostars：https://www.biostars.org/

PacBIo： https://www.pacb.com/blog/genomes-vs-gennnnes-difference-contigs-scaffolds-genome-assemblies/

STHDA： http://www.sthda.com/english/

medscape：https://www.medscape.com/today

教程：

https://www.bioconductor.org/， https://bioconductor.org/help/course-materials/

https://girke.bioinformatics.ucr.edu/GEN242/tutorials/rbasics/rbasics/

https://wikis.utexas.edu/display/bioiteam/Bioinformatics+Team+Home

http://kasperdanielhansen.github.io/genbioconductor/

https://www.ebi.ac.uk/training/on-demand

https://www.petercollingridge.co.uk/tutorials/bioinformatics/

Bioinformatics Training Materials：http://bioinformatics-core-shared-training.github.io/

http://blog.shenwei.me/

http://www.biostathandbook.com/

大学生物信息

Yost Lab at the University of Utah：http://yostlab.genetics.utah.edu/

Gao Lab:http://gsds.cbi.pku.edu.cn/

https://bis.zju.edu.cn/, 简单导航

生物信息工具

Bio Tools: https://bio.tools/

https://bioinf.shenwei.me/，Wei Shen's Bioinformatic tools

http://www.bioinformatics.org/

进化树

iTOL: Interactive Tree Of Life， http://itol.embl.de/

蛋白质

RCSB PDB: https://www.rcsb.org/

ExPASy - ProtParam tool: https://www.expasy.org/， http://web.expasy.org/protparam/

InterPro：https://www.ebi.ac.uk/interpro/entry/pfam/#table

swissmodel: https://swissmodel.expasy.org/interactive

WoLF PSORT: Protein Subcellular Localization Prediction:https://wolfpsort.hgc.jp/

TMHMM Server, v. 2.0: https://services.healthtech.dtu.dk/services/TMHMM-2.0/

SignalP 4.1 Server: http://www.cbs.dtu.dk/services/SignalP/

PredictProtein - Protein Sequence Analysis, Prediction of Structural and Functional Features:https://www.predictprotein.org/

基因结构

GENCOD：https://www.gencodegenes.org/

Gene Ontology Resource ：https://geneontology.org/

ENA: https://www.ebi.ac.uk/genomes/

GDR: https://www.rosaceae.org/

Plant Comparative Genomics：http://www.plantgdb.org/

JGI： https://phytozome-next.jgi.doe.gov/

Genome Browser: http://genome.ucsc.edu/

Gene Structure Display Server 2.0：http://gsds.cbi.pku.edu.cn/index.php

Explore Worm Biology: https://wormbase.org/

microRNA database: https://www.mirbase.org/

ADD GENE： https://www.addgene.org/

KEGG: https://www.genome.jp/kegg/

ENSEMBL：http://asia.ensembl.org/index.html

基因组

WHEAT：https://www.wheatgenome.org/ 、https://wheat.pw.usda.gov/GG3/

COTTON： https://cottonfgd.net/ / https://www.cottongen.org/

https://www.arabidopsis.org/

Promoter 启动子

Web Promoter Scan Service：https://www-bimas.cit.nih.gov/molbio/proscan/

PromoterInspector - highly specific promoter region prediction：http://www.genomatix.de/online_help/help_gems/PromoterInspector_help.html

Promoter 2.0 Prediction Server：http://www.cbs.dtu.dk/services/Promoter/

EPD The Eukaryotic Promoter Database：https://epd.expasy.org/epd/

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PlantCARE, a database of plant promoters and their cis-acting regulatory elements：

http://bioinformatics.psb.ugent.be/webtools/plantcare/html/

Genome Annotation Tools: Promoters-Cis Elements：

http://www.arabidopsis.org/portals/genAnnotation/genome_annotation_tools/cis_element.jsp

Prime引物设计

https://www.ncbi.nlm.nih.gov/tools/primer-blast/

https://pga.mgh.harvard.edu/primerbank/

https://primer3.ut.ee/

http://primer3plus.com/cgi-bin/dev/primer3plus.cgi

Motif

AUGUSTUS Training Server ,Data Input for Running AUGUSTUS: http://bioinf.uni-greifswald.de/webaugustus/prediction/create

https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi

http://meme-suite.org/tools/meme-chip

FGENESH - HMM-based gene structure prediction：

https://www.ebi.ac.uk/Tools/hmmer/search/hmmscan

Blast

URGI Blast Home Page：https://urgi.versailles.inra.fr/blast/

Splign：https://www.ncbi.nlm.nih.gov/sutils/splign/splign.cgi?textpage=online&level=form

MAFFT alignment and NJ / UPGMA phylogeny：http://mafft.cbrc.jp/alignment/server/

weblogo Multiple Sequence Alignment: http://weblogo.berkeley.edu/logo.cgi

http://www.softberry.com/

SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation：https://bioinf.shenwei.me/seqkit/

https://www.rna-seqblog.com/

RNAseq analysis in R；http://combine-australia.github.io/RNAseq-R/

其他工具

https://www.metaboanalyst.ca/faces/ModuleView.xhtml

http://broadinstitute.github.io/picard/explain-flags.html

https://omictools.com/

https://biodbnet-abcc.ncifcrf.gov/db/db2db.php

http://www.drive5.com/

CCNET: http://structuralbiology.cau.edu.cn/gossypium/

Principal Components Analysis Online：https://labriata.github.io/jsinscience/pca/index.html