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   OPEN HELIX Tutorials

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 (tutorialSPS Mart  Fantom5

Genome Browsers

 UCSC Human Genome BioInformatics   

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

NIH RoadMap Epigenomic Browser (tutorial)   WashU EpiGenome   Human Epigenome Atlas   NCBI Epigenomics (help)

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

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 .. BioGPS Gene Annotation

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

ENCODE    GENCODE    RegulomeDB   FANTOM/Gateway (papers / software)

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

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

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

Comparative Toxicogenomics Database (CTD)     NIEHS SNPs   

 

Gene Prediction Tools

GeneMark   AUGUSTUS Gene Prediction Tool (tutorial)  GenScan (info)   Gene Prediction   Melina II (promoter)

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)   miRNA-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 (VEP)   PupaSuite (help, tutorial, exercises)   AVIA  (ref / tutorial)   SNiPA (ref)

SNPnexus (guide) .. PheGenI (tutorial) .. HaploReg v2 (v3) (ref) .. metabolicMine (ref)

CADD .. DANN .. FATHMM (ref) .. GWAVA (ref) .. SusPect (ref) .. F-SNP .. RegulomeDB (GWAS)

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

  rSNP Guide .. rSNPbase (ref / tutorial) .. SNPLogic .. SNP@Ethnos .. SPSMart (comparative frequencies)

 SNPranker (ref) .. DistiLD .. SNPEffect .. pfSNP (ref) .. fitSNPs .. SNPfunc (ref) .. Gene Prospector (ref) .. GRAIL (ref)

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

RVIS Genic Intolerance (ref)

Splice Site SNPs

dbSTEP (ref) .. ssSNPTarget (ref) .. AASsites (ref) .. AS-ALPS (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) .. MutPred .. PMut (ref)  

Cancer Somatic Mutations

 COSMIC (somatic mutations in cancer) .. ICGC .. NCBI Cancer Genome Anatomy Project .. cBioPortal .. CRAVAT (ref / help)

TransFIC    PRISMAD (ref)   BRCA1 Circos (ref)

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

Plateletomics (Platelet transcriptomics by gender)

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

 

Transcription Factor Binding Site Search

TFSEARCH   TransFac   TFBS Search (Qiagen)  TFBS Mapper   TFBIND   MFold  (Basic)   JasPar   PAZAR  

 Swiss Regulon   AR Target Gene Dbase   TESS-discontinued

 

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   HLA-IMP (tutorial/ref)  Genomic Confounding Browser (ref)

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

 

Gene Set Enrichment and Pathway Analysis

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

 Cytoscape    Disease Connect    ToppGene (ref)

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

BioSystems    Pathway Searcher    KEGG    PDB: Biological Process Browser   

GSEA & GSEA-SNP   GIANT (Gene Networks in Tissues; Ref)

 

Gene Ontology

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

 

Proteins

Human Protein Atlas .. ProteomicsDB .. Protein Data Bank .. MOPED .. SWISS-MODEL .. SwissVar .. AS-ALPS (ref)

Phyre 2 (ref; tutorial; tutorial notes)   Phyre 2 Investigator   

 PMut (ref)   SusPect (ref)

PatSearch   UniProt (query)  SwissProt   Protein-Protein Interaction Mining Tool  MINT

 Genome3D  SMART  STRING

Structural Biology Knowledgebase (SBKB)  MEME Suite  

 Post-translational modifications

GPS    PhosSNP (ref)    Functional Glycomics

Protein-related Bioinformatics Resources

 

Human Metabolome Database (HMDB)   metabolicMine (ref)

 ANNOVAR (ref / quick startup guide / AVIA)

AURA: Atlas of UTR Regulatory Activity (ref)

  

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#)  1KG (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)

PPI Mining Tool (Gene Name)   MOPED (Gene)

 GeneCards    Entrez Structure 

Amino Acids   Genetic Code   Ambiguity (Mixed Base) Codes

 BioCompare

 

ONLINE TUTORIALS / TRAINING

EMBER - A Practical Guide to Bioinformatics

Applied Bioinformatics Course (ABC) (ref)

Tutorials: NCBI  Ensembl  UCSC  Haploview  Galaxy  GoldenHelix  ImmPort  Omixon

EMBL-EBI Training

Tutorials @ Open Helix

Online Lectures on Bioinformatics

Getting Genetics Done   BioStars   Swedish Bioinformatics Support (SBS)

 

LINKS

Links to Bioinformatics Tools @ ABC

Bioinformatics.ca

OMICSTools

Online Bioinformatics Resources Collection

 

M.Tevfik Dorak, M.D., Ph.D.

 

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

 

22 May 2015