Bookmarks for Biologists

Online Database/Tools

• NCBI BLAST/Basic Local Alignment Search Tool: Just BLAST.

• Addgene: A database for plasmids and vectors.

• CARD/The Comprehensive Antibiotic Resistance Database: A database for ARGs/ARBs.

• RCSB PDB/Protein Data Bank: A database for protein structures.

• The Jackson Laboratory: A database for mouse models.

• AlphaFold: A database/tool for protein structures predicted by AlphaFold.

• TALEN Designer: A TALEN vector designer.

• UCSF Chimera: A tool for protein 3D structure analysis.

• Benchling: A cloud-based platform for biotech R&D. Similar to SnapGene.

• SignalP: Predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms.

• Bioconductor: A powerful R package for bioinformatics analysis.

• TimeTree: The Timescale of Life: A tool for phylogenetic analysis (for fun).

• Vitascientific.com: Melting Temperature (Tm) Calculation

• NCBI Primer Blast: Primer Designing Tool

• BioRender: A tool to make scientific graphs.

• 国家气象信息中心-中国气象数据网

• 中国气象局国家气候中心

Blogs/Tips/Tutorials

Molecular Cloning

• YouTube Tutorial: Choose Expression Vectors

• AAT Bioquest: Restriction Enzymes Cut Sizes Reference Table

• Blog (CN): 双酶切

• Blog (CN): 蛋白标签_1

• Blog (CN): 蛋白标签_2

• ResearchGate: 3xHA Linker

• Blog (CN): 密码子优化

• Blog (CN): 保护碱基_1

• Blog (CN): 保护碱基_2

• Addgene: Primer Design

• YouTube Tutorial: Primer Design using Benchling

• Blog (CN): 引物设计_知乎

• ResearchGate: Universal Primers vs. Degenerate Primers

• BL21-DE3 Competent Cell Transformation_NEB

• Blog (CN): 质粒的转化

• Plasmid Miniprep

• Alkaline Lysis

• Guide of Analyzing Gel Electrophoresis Results

• Causes of Faint Bands in Gel Electrophoresis

Protein Analysis

• Addgene: Western Blot

• Absorption Spectroscopy

• Ninhydrin Reaction Mechanism

Sequencing

Sanger Sequencing

• Sequencing Chromatograms Interpretation

• DNA Barcoding: Promise and Pitfalls

NGS/Next-Generation Sequencing

• Genomic Data Science_Coursera

• Spacer DNA

• DADA2 Tutorial

• Blog (CN): DADA2 中文教程

• 16s RefSeq Records Processing and Curation

• Bioinformatics_Coursera

• Bioinformatic Methods I_Coursera

• Algorithms for DNA Sequencing_Coursera

• phyloseq: R package for learning microbiome

Quantitative PCR

• Blog (CN): 提升扩增效率_1

• Blog (CN): 提升扩增效率_2

• CRAN: Analysis of qPCR Data, R package

• Publish qPCR data with bar graph_ggplot2

CRISPR

• GPP sgRNA Designer

• GenScript gRNA Design Tool

• Addgene CRISPR

• Thermofisher CRISPR

• Synthego

Pharmacogenomics

• PolyPhen-2: A tool for prediction of functional effects of human nsSNPs.

• PROVEAN: A database for prediction of protein functional changes.

• NCBI-dbSNP: A mutation database.

• PharmVar/Pharmacogene Variation Consortium: A database for drug-related genes.

• CPIC/Clinical Pharmacogenetics Implementation Consortium: A database for drug-related genes.

• PharmGKB: A database for drug-related genes.

Drug Crystallization

• XRPD/X-Ray Powder Diffraction

• Blog (CN): XRPD:布拉格定律

• DSC/Differential Scanning Calorimetry

• Blog (CN): 热重分析

Others

• 讯飞听见: Transcribe audios into words.

• Reddit subreddit/labrats: A forum for biology-related discussions.