HLA MHC Inf & Imm Genetics Evolution Biostatistics
Population
Genetics Genetic Epidemiology Homepage
BIOINFORMATICS TOOLS
M.Tevfik DORAK
" HFE Links "
NCBI Global Database Search NCBI Resources Tutorials NIH Helix
NCBI
Tools for Data
Mining
Gene .. GeneMap .. GenAtlas .. GenCanVas .. GeneLynx .. iHOP .. ExPASy
NCBI .. BLAST .. e-PCR .. GeneNote .. GeneCards .. GeneLoc .. CGAP-GAI
Ensembl
Genome Browser (Human) .. Vega Genome Browser (Human) .. eGenome
HapMap HapMap Genome
Browser-B36
USCS Human Genome BioInformatics
Database
of Genomic Variants (CNV) Copy
Number Variation Resources DECIPHER
OMIM .. OMIM Map .. NCBI
Genetic Association Database .. HuGE Navigator .. NCBI dbGaP
GeneMAPP (Gene
Pathway Profiler) .. NetAffX
Gene
Expression Atlas .. ArrayExpress .. Genevar .. Gene
Expression Omnibus (GEO)
EC Gene
(alternative splicing) .. SOURCE (genomics
tool) .. COSMIC (somatic mutations in cancer)
SNP Resources
Variation
Discovery Resource UW-FHCRC (
dbSNP
.. dbSNP Tutorial .. SNP500
Cancer .. HGBASE .. HGMD .. SNPseek
(Batch Analysis; Ch6)
GeneSNPs .. rSNP Guide .. SNPEffect .. SNP@Ethnos .. Haploplotter
FastSNP .. FastSNP Novel SNP Analysis
.. stSNP .. MutDB .. SiPEP .. VaryGene
SNPs3D .. PolyPhen
Prediction of Functional Effect of Human nsSNPs
(by cSNP) .. SIFT (by
SNP ID)
PolyDoms .. Panther (Download) .. Pmut .. PupaSuite (Help, Tutorial, Exercises)
Software and Databases for SNP Research
WGAviewer
(Ge, 2008; Workshop Notes)
TaqMan SNP Genotyping Assays Affymetrix & Quick Query
Transcription Element Search Software (TESS)
Searching
TF Binding Sites .. TransFac .. MFold
(Basic)
SNPtagger .. SNP HaploTag Calculator .. HaploBlockFinder
NCBI Cancer Genome Anatomy
Project Pathway Searcher KEGG
Chang
Bioscience Tools VISTA
Tools
Roche Application Notes ..
BioTechniques Protocol Guide 2008
Molecular
Biology Notebook .. Mol
Biol Methods FAQ
Mol Biol
Resources
.. Mol Biol
Protocols (1) .. HIV-Sequence
Database
Ambion
Technical Library .. Access
Biotech
Restriction Enzyme Database .. Restriction Mappers .. Blast REbase .. NEBCutter
Primer Design
Software
.. BatchPrimer3 .. Tm determination .. Oligo Analyser and PrimerQuest (IDT)
Quantitative PCR Primer Database - QPPD (NCI)
Sequence Analysis .. Tools for Working with Sequences .. OSA Seq Analysis Software .. OEGE Sequence Tools
Multiple Sequence Alignment: ClustalW (help) .. BCM .. BioEdit .. Topali v2
Expasy
Translate Tool .. EMBL
Translation Machine .. JustBio Bioinformatics
ORF Finder (NCBI) .. Tools
for Data Mining (NCBI) .. NCBI
Site Map .. dbMHC
MHC Gene Table (Sanger) Annotated MHC Gene List (Shiina, 2004)
Search
Templates
Gene (Gene Name) Gene (GeneID) dbSNP (GeneID) dbSNP (rs#) Vega / Ensembl (Gene Name) Ensembl (SNP)
HapMap (SNP)
HapMap (Gene)
GAD (Gene Name) HGMD
(Gene Name) PolyPhen (SNP) MutDB (Gene ID)
SNPs3D Candidate Genes List for Disease SNPs3D
GeneCards Entrez Structure
(BioInfoBank)
IMGT/HLA MICA
IMGT/HLA Cell Line IMGT/HLA
Allele Query
Amino Acids Genetic Code
Ambiguity Codes
NOMENCLATURE GUIDES
http://www.gene.ucl.ac.uk/nomenclature 2002
Human Gene Mutation Nomenclature (mirror) Human Gene Nomenclature Search Genomic Variation Databases
Ig and TCR nomenclature Entrez Gene Mouse Genetic Nomenclature
General Allele
Frequency Database ALFRED HLA Allele
Frequencies
M.Tevfik Dorak, M.D., Ph.D.
HLA MHC Inf & Imm Genetics Evolution
Biostatistics Population Genetics Genetic Epidemiology Homepage
15
Aug 2008