HLA MHC Inf & Imm Genetics Evolution Biostatistics Population Genetics Genetic Epidemiology Homepage
BIOINFORMATICS TOOLS
M.Tevfik DORAK
" HFE Links "
Bioinformatics Links Directory OpenHelix Tutorials
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 .. In Silico PCR .. GeneNote .. GeneCards .. GeneLoc .. CGAP-GAI
Ensembl Genome Browser (Human) .. Vega Genome Browser (Human) .. eGenome
HapMap HapMap Genome Browser-B36 (2008) (2009) (2010)
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 .. DAVID
SNPtagger .. SNP HaploTag Calculator .. HaploBlockFinder
GeneMAPP (Gene Pathway Profiler) .. NetAffX .. Gene Exp Atlas .. ArrayExpress .. Gene Exp Omnibus (GEO)
EC Gene (alternative splicing) .. SOURCE (genomics tool) .. COSMIC (somatic mutations in cancer)
miRBase NCBI Epigenomics Browser (Help)
SNP Resources
Variation Discovery Resource UW-FHCRC (Seattle SNPs -Tutorial): VG2 (Visual Genotypes)
GVS .. PERLEGEN .. USCS .. Br1958BC
F-SNP .. SCAN .. SNPxGE2 .. seeQTL .. Genevar .. PhenGenI .. RegulomeDB (GWAS)
dbSNP .. dbSNP Tutorial .. SNP500 Cancer .. HGBASE .. HGMD .. Diseasome (SNPs & Disease)
SNPnexus .. SNPedia .. NextBio .. SNPwatch .. MedRefSNP .. SNP Control .. MutaGeneSys .. LS-SNP/PDB
GeneSNPs .. rSNP Guide .. SNPEffect .. SNPLogic .. 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 & HWE OEGE HWE Calculator
TaqMan SNP Genotyping Assays Affymetrix & Quick Query
WGAviewer (Ge, 2008; Workshop Notes)
GWAS:
GWASdb Catalog (NIH) Database (Japan) Johnson & O'Donnell, 2009
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 .. Blast REbase .. NEBCutter
Primer Design Resources .. SNP_Cutter & SNP-RFLPing (PCR-RFLP Design)
Primer Design Software Primer3 (Help) .. Primer3Plus .. BatchPrimer3 (Help - Ref) .. Viz-Primer
Oligo Analyser and PrimerQuest (IDT)
Primer - Probe Design Software List .. FastPCR (free) .. FastPCR Online Tools .. In Silico PCR
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 .. Jabaws
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#) GWAS Cat (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
HLA MHC Inf & Imm Genetics Evolution Biostatistics Population Genetics Genetic Epidemiology Homepage
July 13, 2012