Dr. Wei Li's Laboratory
Institute of Genetics and Developmental Biology
Chinese Academy of Sciences, Beijing, China

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

• GOOGLE
• NCBI Entrez
• EBI SRS
• E-BioSci

• NCBI Home Page
• ExPaSy Life Science Resources
• ExPASy Proteomics Server
• Broad Institute Resources
• NCBI Human Genome Resources
• NCBI Mouse Genome Resources
• NAR databases
• EBI Toolboxs
• NG Web Resources
• CMS
• DNA Sequence & Structural Analyses
• Biocatalog

• NCBI Genome Browser
• UCSC Genome Browser Gateway
• Ensembl Genome Browser
• GDB Human Genome Database
• MGI Mouse Genome Database
• Rat Genome Database
• Flybase Fruitfly 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
• BLAST 2 Sequences (Compare two sequences)
• BLAT Search (Locate your sequence in Genome)
• Spidey-- mRNA to genomic alignment
• MEME -Conserved Motif
• ClustalW - multiple sequence alignment (MSA)
• T-COFFEE- MSA
• CINEMA- MSA editor
• GeneDoc
• BoxShade
• Repeats Masker
• RU - Repeats Database

• PubMed
• OMIM
• iHOP -abstract search
• HGMD -Human Gene Mutation Database
• DBGET -Protein mutation
• MMBID - Inherited Disease
• FIDD -disease frequencies
• ALFRED -allele frequencies
• HapMap
• HGVbase - Human Gene Variation Database
• Disease-centered mutation
• GeneTests
• NCBI Cancer Genome Anatomy
• Atlas Chromosomes in Cancer
• Online Medical Dictionary
• Medical Encyclopedia
• Hermansky-Pudlak Syndrome Database (HPSD)

• NCBI Entrez Gene
• UCSC Gene Sorter
• Wizmann GeneCards (Human Gene)
• FANTOM3: Mouse Functional Genomics
• KEGG GENES
• euGenes: Eukaryote Genes
• Map Viewer -mapping a gene

• Genescan
• GeneID
• Pseudogenes
• HomoloGene
• HOVERGEN

• NCBI Reference Sequence (RefSeq)
• NCBI ORF Finder
• GNF Gene Expression Atlas (SymAtlas )
• NCBI Gene Expression Omnibus (GEO)
• Database Of Transcribed Sequences (DoTS)
• CONREAL Server (conserved regulatory elements)
• Transcription Factor Search
• ConSite
• Promoter Scan
• Kozak Predictor
• Exonic Splicing Enhencer finder
• NetGene2 -splicing site
• MGED - Microarray Society
• Microarray data analysis
• Microarray datasets

1. Protein Prediction

   1. Properties

      • MW and PI
      • SWISS-2DPAGE
      • Signal Peptide
      • Phosphorylation Sites
      • GPI Modification Site
      • GalNAc O-glycosylation sites

   2. Domains and Motifs

      • Scan PROSITE (NPS)
      • Scan InterPro
      • NCBI Conserved Domain
      • Motif Scan
      • SMART - Simple Modular Architecture Research Tool
      • PSORT II (Sorting Signal and Localization Sites)

   3. Structure - 2D and Topology

      • PredictPROTEIN
      • HMMTOP -transmembrane helices
      • SOSUI -transmembrane helices
      • TMHMM - transmembrane helices
      • TMpred - transmembrane helices
      • TopPred 2- transmembrane helices
      • Membrane Protein Explorer (MPEx)
      • Coiled COILS
      • SOPMA 2D
      • PSIPRED - 2D and fold recognition
      • Evaluation of structure prediction

   4. Structure - 3D Modeling

      • SWISS-MODEL
      • 3D-PSSM
      • SPARKS
      • SAM-T02
      • GENO3D
      • Cn3D
      • 3D Comparison
      • 3D Softwares
      • PDB2MultiGif
      • Protein Explorer
      • RasMol
      • MolVis Resources - DeepView
      • WebMol - Java PDB Viewer
      • MolScript - 3D Displaying

2. Protein Database and Retrieval

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

   1. Protein Family

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

   2. Protein Structure

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

   3. Protein Interaction

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

   4. Protein Pathway

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

• Linkage software list
• Genehunter
• APM
• GOLD
• WebQTL
• Map Manager QTX
• ASP/HAPMAX
• Progeny - Pedigree
• Family History
• PediDraw

• Major Resources
• The Jackson Laboratory
• BACPAC
• mymouse.org Home
• Transgenic Animal Models
• Transgenic Mouse Facility
• Gene Knockouts
• GeneTrap
• Combined Mouse/Human Phenotypes
• Mouse Brain Gene Expression Map
• LOCATE: Mouse Gene Location

1. Tools

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

2. References

   • BLAST program selection guide
   • Proteomics - Protocols
   • Ambion_siRNA and RNAi Resource
   • Microarray Analysis References
   • bibliography: QTL
   • HUGO Gene Nomenclature Committee
   • Glossary in Genomics and Genetics
   • Genetics Education Center
   • Genetic Science Learning Center
   • SPECIES 2000
   • Tree of Life

1. Antibodies

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

2. Biotech

   • Affymetrix
   • Ambion Inc.
   • Amersham Biosciences
   • BD_Clontech
   • Beckman Coulter
   • Calbiochem
   • Invitrogen
   • Mirus siRNA
   • New England Biolabs
   • Novagen
   • PIERCE
   • Roche
   • QIAGEN
   • Santa Cruz
   • Sigma-Aldrich.com
   • Stratagene
   • Upstate
   • USB

3. Genetics

   • Applera
   • Astex
   • Biotage AB
   • Celera
   • Genaissance
   • GeneSifter
   • Genzyme
   • Illumina
   • Myriad
   • Orchid
   • SEQUENOM
   • THIRD WAVE

4. misc.

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

• Dr. Liang-Biao Chen's Lab
• Dr. Jing-Dong Han's Lab
• Dr. Wei Li's Lab
• Dr.Yong-Biao Xue's Lab

• GUCAS--Signal Transduction

  • Presentation: Vesicle Trafficking-PDF file
  • Reference 1
  • Reference 2

• GUCAS--Molecular Systems Biology

• Presentation: Linkage & Association
• Reference 1
• Reference 2

• Summer Course--Medical Genetics

• Presentation: Positional Cloning

• IGDB Graduate Course--Developmental Biology

  • Presentation: Mouse Genetics
  Reference 1
  Reference 2

• Chinese Academy of Agriculture--Molecular Genetics

  • Presentation: Genes & Diseases