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 (Seattle SNPs -Tutorial): VG2 (Visual Genotypes)

GVS ,, PERLEGEN .. USCS

dbSNP .. dbSNP Tutorial .. SNP500 Cancer .. HGBASE .. HGMD .. SNPseek (Batch Analysis; Ch6)

MutaGeneSys .. SNPedia

 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

HWE & SNP Association

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

UniProt / SwissProt

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)

Primer - Probe Design

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

 BioCompare

 

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