Dr. Wei Li's Laboratory
Beijing Children's Hospital, Capital Medical University

Table

• Search Engines
• Web Resources
• Genome Bioinformatcs
• Sequence Bioinformatcs
• Medical Bioinformatics
• Composite Gene Information
• Gene Prediction and Homologues
• Transcriptomics
• Proteomics
• Genetic Analysis
• MOUSE resourses
• Lab Tools and References
• Lab Suppliers
• IGDB Bioinformatics Consortium
• Dr. Wei Li's Graduate Course Materials

• NCBI Entrez
• EBI SRS

• NCBI Home Page
• ExPaSy Life Science Resources
• NCBI Human Genome Resources
• NCBI Mouse Genome Resources
• NAR databases
• EBI Toolboxs
• Biocatalog

• NCBI Genome Browser
• UCSC Genome Browser Gateway
• Ensembl Genome Browser
• MGI Mouse Genome Database
• Ensembl Zebrafish Genome Browser
• Wormbase Worm Genome Database
• SGD Yeast Genome Database
• TAIR Arabidopsis Genome Database

• NCBI GenBank (Nucleotide)
• NCBI GenBank (Protein)
• BLAST Search
• FASTA Search
• BLAT Search (Locate your sequence in Genome)
• MEME -Conserved Motif
• ClustalW - multiple sequence alignment (MSA)
• CINEMA- MSA editor
• BoxShade
• Repeats Masker
• RU - Repeats Database

• PubMed
• OMIM
• HGMD -Human Gene Mutation Database
• ClinVar
• ClinGen
• dbSNP
• 1000 genome
• ExAC-exomes
• DECIPHER
• dbVAR-chromosome variants
• GWAS
• MITOMAP-mitochondial genome
• ALFRED -allele frequencies
• HGVS-mutation nomenclature
• HGVbase - Human Gene Variation Database
• NCBI Cancer Genome Anatomy
• Medical Encyclopedia
• GeneReviews
• MalaCards-Human Disease Database
• Hermansky-Pudlak Syndrome Database (HPSD)
• CGCN-Genetic Counseling

• NCBI Entrez Gene
• UCSC Gene Sorter
• Wizmann GeneCards (Human Gene)
• KEGG GENES
• euGenes: Eukaryote Genes
• Map Viewer -mapping a gene

• Genescan
• Pseudogenes
• HomoloGene
• HOVERGEN
• Gene Names

• NCBI Reference Sequence (RefSeq)
• NCBI ORF Finder
• GNF Gene Expression Atlas (SymAtlas )
• NCBI Gene Expression Omnibus (GEO)
• Genome RNAi
• Promoter Scan
• Exonic Splicing Enhencer finder
• NetGene2 -splicing site

1. Protein Prediction

   1. Properties

      • MW and PI
      • SWISS-2DPAGE
      • Peptide Atlas
      • GalNAc O-glycosylation sites

   2. Domains and Motifs

      • Scan InterPro
      • NCBI Conserved Domain
      • SMART - Simple Modular Architecture Research Tool

   3. Structure - 2D and Topology

      • HMMTOP -transmembrane helices
      • TMpred - transmembrane helices
      • Membrane Protein Explorer (MPEx)
      • Coiled COILS
      • SOPMA 2D
      • PSIPRED - 2D and fold recognition
      • InBio Map
      • IID

   4. Structure - 3D Modeling

      • SWISS-MODEL
      • GENO3D
      • Cn3D
      • 3D Comparison
      • 3D Softwares
      • RasMol

2. Protein Database and Retrieval

   • ExPASy - Swiss-Prot
   • UniProtKB
   • PIR - Protein Information Resources
   • PRIDE: Proteomics

   1. Protein Family

      • Pfam -Protein Families Database
      • COG
      • Enzyme Names
      • BRENDA - Enzyme Database
      • PHYLIP -phylogeny

   2. Protein Structure

      • PDB - Protein Data Bank
      • SCOP - Domains
      • CATH - Domains
      • InterPro - Domains
      • PRINTS - motifs
      • Superfamily
      • ModBase
      • BMRB - NMR structure

   3. Protein Interaction

      • HPRD
      • BioGRID
      • DIP
      • MIPS - Mammalian PPI
      • YEAST GRID
      • MIPS- yeast
      • DroID- fly
      • Worm
      • KEGG LIGAND
      • STRING
      • PubGene
      • PPI Finder

   4. Protein Pathway

      • KEGG Pathway
      • EcoCyc - E Coli
      • Gene Ontology
      • STKE - Signal Transduction Patyway
      • SPIKE-Signaling

• SIFT
• PolyPhen2
• Mutation Taster
• Linkage software list
• APM
• GOLD
• ASP/HAPMAX
• Progeny - Pedigree
• Family History
• PediDraw

• The Jackson Laboratory
• mymouse.org Home
• Transgenic Mouse Facility
• Combined Mouse/Human Phenotypes
• LOCATE: Mouse Gene Location

1. Tools

   • Primer Design
   • Primer3
   • Webcutter - DNA restriction site
   • DNA Restriction Map
   • Peptide Cutter
   • Peptide Mass
   • Translation Machine
   • DNA Conversion and Protein Translation
   • Ambion siRNA Search

2. References

   • BLAST program selection guide
   • Ambion_siRNA and RNAi Resource
   • Microarray Analysis References
   • bibliography: QTL
   • Glossary in Genomics and Genetics
   • Genetics Education Center
   • SPECIES 2000
   • Tree of Life

1. Antibodies

   • Aves Labs - Custom Chicken Antibodies
   • Rockland Antibodies
   • Transduction Antibodies
   • Washington Custom Antibodies

2. Biotech

   • Affymetrix
   • Ambion Inc.
   • BD_Clontech
   • Calbiochem
   • Invitrogen
   • Novagen
   • PIERCE
   • Roche
   • QIAGEN
   • Santa Cruz
   • Sigma-Aldrich

3. Genetics

   • Biotage AB
   • Quest
   • GeneSifter
   • Illumina
   • SEQUENOM
   • SoftGenetics
   • Novogene
   • Chigene

4. misc.

   • Pharmaceutical Suppliers List
   • Labvantage-LIMS
   • LIMS-genotyping

• American Society for Cell Biology
• American Society of Human Genetics
• Chinese Society for Cell Biology
• Genetic Society of China
• Chinese Neuroscience Society
• The Biophysical Society of China
• Chinese Association for Physiological Sciences
• The Ministry of Science and Technology of the Peopleos Republic of China (MOST)
• Ministry of Agriculture of the Peopleos Republic of China (MOA)
• Ministry of Health of the Peopleos Republic of China (MOH)
• The National Natural Science Foundation of China (NSFC)
• Bioscience Reports
• Journal of Genetics and Genomics
• Hereditas (Beijing)

• GUCAS--Signal Transduction

• IGDB Graduate Courses