HLA     MHC    Inf & Imm    Genetics     Evolution     Biostatistics     Population Genetics    Genetic Epidemiology    Homepage

 

BIOINFORMATICS TOOLS

Mehmet Tevfik DORAK, MD PhD

 

EMBER - A Practical Guide to Bioinformatics

Online Suites

Galaxy (101 - Support)   ExPASy (ref)   Taverna (ref)   BioMart (ref)   Artemis (manual)   Babelomics (ref / tutorial)   Bioconductor (manual)

Biomarts

Ensembl BioMart (YouTube tutorial)   UCSC Table Browser   HapMap BioMart   GWAS Central GWAS Mart   SPS Mart 

Genome Browsers

 UCSC Human Genome BioInformatics   

Ensembl Genome Browser (Human)   Vega Genome Browser (Human)

NIH RoadMap Epigenomic Browser (tutorial)   Human Epigenome Atlas   NCBI Epigenomics (h) / Browser

HapMap Genome Browser   1KG (Browser - Quick Start Guide)-(NCBI)   GENCODE Browser   VaDE

CNV Browser   eQTL Browser   StarBase (tutorial / ref)   NextBio Browser   Integrative Genomics Browser

VISTA Enhancer Browser    Swiss Regulon   lncRNome   Reactome Pathway Browser

 

NCBI Global Search   GoPubMed  HuGE  LabMeeting   NCBI Tutorials / Handbook / Help Manual   NIH Helix   NCBI Tools for Data Mining 

Sanger: Software / Databases

Gene .. GeneMap .. GenAtlas .. GenCanVas .. GeneLynx .. iHOP .. GeneCards .. NetAffX .. Gene Exp Atlas

NCBI (tutorials on YouTube) .. BLAST .. e-PCR .. In Silico PCR .. GeneNote .. GeneLoc .. CGAP-GAI .. Aceview

ENCODE    GENCODE    RegulomeDB   CADD    FANTOM (papers / software)

Database of Genomic Variants (CNV)   Copy Number Variation Resources   DECIPHER

OMIM .. OMIM Map .. NCBI Genetic Association Database (GAD) .. HuGE Navigator  

Gene Exp Omnibus -GEO (NCBI) .. NCBI dbGaP .. ArrayExpress (EBI) ..  SOURCE (genomics tool)

Comparative Toxicogenomics Database (CTD)     NIEHS SNPs   

 

Gene Prediction Tools

GeneMark   AUGUSTUS Gene Prediction Tool (tutorial)  GenScan (info)   Gene Prediction

Rfam (RNA sequence families of structural RNAs) Prediction Tool   moses (ncRNA) 

EC Gene (alternative splicing) .. NNSplice (splice site prediction on genomic sequence) .. ssSNPTarget (ref)

 

microRNA/ncRNA Resources

 miRBase  miRDB  mrSNP  TargetScan  dPORE-miRNA  miREnvironment  StarBase  microSNiPer (refDIANA-TarBase

 Human miRNA Disease Database (HMDD)   miRCancer   OncomiRDB (ref)   HOCTAR (refFAME (ref)   IntaRNA (ref / help)

lncRNA and Disease Database   lncRNA-SNP db (ref)   ncRNA Databases Resource (NRDR)  

 lncRNome (ref / user guide)   LncRBase (ref)   NONCODE (ref)   PseudoMap (ref / tutorial)

 NHGRI Histone Database 

 

SNP Resources (variation & functional annotation)

GENEPI TOOLBOX (ref)   G2D (Genes to Disease; ref / tutorial)   Gene Prioritization Tool (ref)   Endeavour

Links to Gene Prioritization Tools

dbSNP .. dbSNP Tutorial .. Variation Discovery Resource UW-FHCRC (Seattle SNPs): VG2 (Visual Genotypes)

NCBI Variation Viewer   NCBI ClinVar   NHGRI Clin Genomic DB   SNP500 Cancer   GeneSNPs   PharmGKB

 Ensembl Variant Effect Predictor   PupaSuite (help, tutorial, exercises)

SNPnexus (guide) .. PheGenI (tutorial) .. RegulomeDB (GWAS) .. HaploReg v2 (v3) (ref) .. CADD .. F-SNP  

VarioWatch .. SNPedia .. NextBio .. SNPwatch .. MedRefSNP .. SNP Control .. MutaGeneSys .. LS-SNP/PDB

  rSNP Guide.. SNPLogic .. SNP@Ethnos .. SNPranker (ref) .. DistiLD .. SNPEffect .. Gene Prospector (ref) .. GRAIL (ref)

Haplotter   Selectome - A Database of Positive Selection   dbPSHP (ref)   GERP (ref1 / ref2)

Splice Site SNPs

dbSTEP (ref) .. ssSNPTarget (ref)

Coding SNP Annotation

SNPs3D .. dbNSFP (ref) .. MSV3d (ref) .. SNPdbe (ref) .. PolyPhen-2 .. SIFT (by SNP ID) .. PolyDoms .. SNPdryad (ref) .. KD4v (ref)

 MutDB .. HGMD .. Panther (download) .. FannsDB (Condel & TransFIC) .. Mutation Assessor (ref)

Cancer Somatic Mutations

 COSMIC (somatic mutations in cancer) .. ICGC .. NCBI Cancer Genome Anatomy Project .. cBioPortal .. TransFIC  

eQTL Resources

GTEx .. NCBI eQTL Browser .. SCAN (tutorial) .. Genevar (eQTL/mQTL) .. PheGenI  

eQTL Resources @ Pritchard Lab (browser) .. Blood eQTL Browser

SNPexp .. SNPexpress .. SNPxGE2 (ref / tutorial) .. seeQTL

Proxy Search

ssSNPer .. SNAP .. SNPSnap (ref / guide) .. GLIDERS .. SPOT (ref / user guide) .. HaploReg v2 (v3) .. CandiSNPer (ref) .. VaDE

SNP Data Analysis (including HWE): SNPStats   HWE  OEGE HWE Calculator

 

GWAS Resources

 GWASdb    Catalog (NIH)   dbGAP Association Results Browser   GWAS Central   HuGE GWAS Integrator   Database (Japan) 

GRASP (ref / overview / user guide)   GWATCH (ref / tutorial)   GWAS3D (ref)   VaDE

 Johnson & O'Donnell, 2009   WGAviewer (ref / workshop notes)   GenAMap (ref / tutorial)   SNPTrack (ref)

OMICtools   LocusZoom (ref)   GWAS Diagram Browser   SIB Association Viewer (ref)

SNP Imputability   Genomic Confounding Browser (ref)

Breast Cancer GWAS: GAME-ON   CGEMS   (KM Plotter)

 

Gene Set Enrichment Analysis

DAVID (ref / tutorial) .. PANOGA (ref / tutorial) .. IPAD (ref) .. SSEA (ref) .. See also Huang, 2009

 Cytoscape    Disease Connect    ToppGene

UniHi .. Reactome (user guide) .. BioCarta .. GeneMAPP (Gene Pathway Profiler) (tutorial) .. GSEA/MSigDB

BioSystems    Pathway Searcher    KEGG    PDB: Biological Process Browser

GSEA & GSEA-SNP

Gene Ontology

QuickGO (ontology) .. Gene Ontology (AmiGO browser)

 

Software and Databases for SNP Research   ANNOVAR (ref / quick startup guide)

AURA: Atlas of UTR Regulatory Activity (ref)

 Gene Regulation Databases   Plateletomics (Platelet Transcriptomics by Gender)

Human Metabolome Database (HMDB) .. Human Protein Atlas .. ProteomicsDB .. Protein Data Bank

Transcription Element Search Software (TESS)-discontinued

Searching TF Binding Sites   TransFac    MFold  (Basic)   Mapper   JasPar   PAZAR   Swiss Regulon   AR Target Gene Dbase

PatSearch   UniProt / SwissProt

STR Database

 TaqMan SNP Genotyping Assays (1)  (2)  

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 .. 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 .. ORF Finder (NCBI) .. JustBio Bioinformatics Tools  

Chromosome 6 (Sanger)   MHC Haplotype Project   Annotated MHC Gene List (Shiina, 2004)  

IMGT/HLA MICA   IMGT/HLA Cell Line   IMGT/HLA Allele Query   dbMHC   ImmPort

Genomic coordinate conversion: Ensembl Assembly Converter   Kaviar

 

Search Templates

Gene (Gene Name1/Human)  Gene (Gene Name2)  Gene (GeneID)  dbSNP (GeneID)  dbSNP (rs#)  NextBio (rs#) 

GWAS Cat (rs#)   GWAS Central (rs#)   GTeX (Gene Name)

Variation Viewer (geneName)   Variation Viewer (rs#)   Broad Institute (rs#)   VaDE (rs#)

Vega / Ensembl (Gene Name)  Ensembl (SNP)  HapMap (SNP)  1KG (Gene)  HapMap (Gene)  HapMap (chrX)  HapMap (chrY)  SNPedia (rs#)

RegulomeDB (chr#/nt#)  dbSTEP (chr#; nt#)  Genomic Confounding Browser (rs#)

COSMIC Gene Analysis Search Template (by Gene Name)

mirBase microRNA search (chr coordinates)

Qiagen/SABiosciences TFBS search (Gene Name)

 GAD (Gene Name)   HGMD (Gene Name)   PolyPhen (SNP)  MutDB (Gene ID)

 SNPs3D Candidate Genes List for Disease   SNPs3D

 GeneCards    Entrez Structure   (BioInfoBank)

Amino Acids   Genetic Code   Ambiguity Codes

 BioCompare

 

ONLINE TUTORIALS

EMBER - A Practical Guide to Bioinformatics

Applied Bioinformatics Course (ABC) (ref)  

Tutorials: NCBI  Ensembl  UCSC  Haploview  Galaxy  GoldenHelix  ImmPort  Omixon

EMBL-EBI Training Workshops

Tutorials @ Open Helix

Online Lectures on Bioinformatics

Getting Genetics Done   BioStars   Swedish Bioinformatics Support (SBS)

 

LINKS

Links to Bioinformatics Tools @ ABC

Bioinformatics.ca

OMICSTools

 

 

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

 

17 February 2015