HLA MHC Inf & Imm
Genetics Evolution
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BIOINFORMATICS TOOLS
M.Tevfik DORAK
" HFE Links "
Bioinformatics Links Directory
NCBI
Global Search GoPubMed LabMeeting NCBI 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 (2008) (2009)
USCS Human Genome BioInformatics STR
Database
Database of Genomic Variants (CNV) Copy
Number Variation Resources DECIPHER
OMIM .. OMIM Map .. NCBI
Genetic Association Database .. HuGE Navigator .. NCBI dbGaP
SNPtagger .. SNP HaploTag Calculator .. HaploBlockFinder
GeneMAPP (Gene
Pathway Profiler) .. NetAffX .. Gene Exp
Atlas .. ArrayExpress .. Genevar .. Gene Exp
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)
SNPnexus .. SNPedia .. NextBio .. SNPwatch .. MedRefSNP .. SNP
Control .. MutaGeneSys .. LS-SNP/PDB
GeneSNPs .. rSNP Guide .. SNPEffect .. F-SNP .. SNP@Ethnos .. Haplotter
FastSNP .. FastSNP Novel SNP Analysis ..
stSNP .. MutDB .. SiPEP .. VaryGene .. QuickGO (ontology)
SNPs3D .. PolyPhen Prediction of Functional Effect of Human nsSNPs (by cSNP) .. SIFT (by
SNP ID) .. SCAN
PolyDoms .. Panther (Download) .. Pmut .. PupaSuite (Help, Tutorial, Exercises)
Software and Databases for SNP Research
SNP Data Analysis
(including HWE): SNPStats & HWA
TaqMan SNP Genotyping Assays Affymetrix & Quick Query
WGAviewer (Ge, 2008;
Workshop Notes)
GWAS:
Catalog
(NIH), Database (Japan)
Transcription
Element Search Software (TESS)
Searching TF Binding Sites TransFac MFold
(Basic)
Mapper
JasPar
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)
Vassar Online Statistics
Search Templates
Gene (Gene Name1) Gene (GeneName2) Gene (GeneID) dbSNP (GeneID) dbSNP (rs#) NextBio (rs#)
Vega / Ensembl (Gene Name) Ensembl (SNP) HapMap (SNP) HapMap (Gene) SNPedia (rs#)
ABI TaqMan (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
Tutorials:
Ensembl Haploview GVS
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
11 January 2010