HLA     MHC    Genetics     Evolution     Biostatistics     Population Genetics    Genetic Epidemiology    Homepage

 

BIOINFORMATICS TOOLS

(for Genetic Epidemiologists)

Mehmet Tevfik DORAK, M.D., Ph.D.

 

Open Access Reviews

ENCODE Resources (Pazin MJ. CSHP 2015); Database Tools (Bianco, Genomics 2013; Zou, 2015); UCSC Browser (Mangan, 2014)

JournalsNucleic Acids Research: Database Issue (2017)Web Server Issue (2016);  Database: Biomart IssueEnsembl Issue

 Nucleic Acids Research Databases Catalog

 

Societies

ISCB     ISMB    AMIA 

 

Online Suites

Galaxy (101 - Support)   ExPASy (ref)   Taverna 2.5.0/Archive (ref)   Apache-Taverna   BioMart (ref)   Artemis (manual)   Babelomics (ref / tutorial)  

Bioconductor (manual)   BioPython (tutorial & cookbook / PDF)

EDGE: Empowering the Development of Genomics Expertise (ref)

 

Biomarts

Ensembl BioMart (YouTube tutorial)   UCSC Table Browser   GWAS Central GWAS Mart (tutorial)   SPS Mart (allele freqs)  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)   NGSmethDB (ref)

1KG (Browser - Quick Start Guide)-(NCBI)   UK10K (ref)   GENCODE Browser   SNiPA

CNV Browser  DECIPHER  eQTL Browser  seeQTL  GTEx eQTL Browser

StarBase (tutorial / reflncRNome  lncRBase  NonCode   Integrative Genomics  

VISTA Enhancer Browser    Swiss Regulon    Reactome Pathway Browser   ImmunoBase Browser  

 

 General Resources

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

Sanger: Software / Databases     EMBL-EBI    Swiss Institute of Bioinformatics: ExPASy

NCBI Gene .. GeneCards .. GeneMap .. GenAtlas .. GenCanVas .. iHOP .. NetAffX .. BioGPS Gene Annotation

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

ENCODE (ref)   GENCODE    RegulomeDB   FANTOM/Gateway (papers / software)

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

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

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

Comparative Toxicogenomics Database (CTD)   NIEHS SNPs    RNA-seq Atlas (ref)   NGSmethDB (ref)  

Genomic coordinate conversion: Ensembl Assembly Converter   Kaviar

rsID to VCF conversion: dbSNP   

 

ncRNA (microRNA/lncRNA) & Pseudogene Resources

NONCODE (ref)   NPInter v3 (ref)   ncRNA Databases Resource (NRDR)   ChIPBase (ref)

 miRBase   miRDB   mrSNP   TargetScan   miRWalk 2.0 (ref)  StarBase (tutorial / ref)   miRNA SNiPer (ref)   microSNiPer (ref

DIANA-TarBase (ref)    miRTarBase (ref-2014 / 2016)   miRmap (ref)   miRNAmap (tutorial/ref)   Human miRNA Tissue Atlas (ref)   miRFocus   

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

RegNetwork (TF and miRNA networks) (ref)    Genome-wide Predictions of miRNA Regulation by Transcription Factors Database  (ref)

miRNA-SNP db (ref)   AVIA miR SNP Analysis Tool   miTranscriptome (ref

 

FANTOM CAT/lncRNA Atlas (ref)

lncRNA and Disease Database   Human lincRNA catalog (Broad)    lncRNA2Target (ref)   lncReg (ref)   lncTar for Target Prediction (ref)

 lncRNome (ref / user guide)   LNCiPedia (ref)  lncRBase (ref)   DIANA-lncBase (ref / v2.0)   lncRNAtor (ref)   lncRNAdb    LncRNADisease (ref)

lnCaNet Database (lncRNA-Cancer co-expression database) (ref)   co-lncRNA (ref

 lncRNA-SNP db (ref)   LincSNP v2.0 (ref)   lncRNASNP (ref)

 

Database of small human noncoding RNAs (DASHR) (ref)    miRVaS (miRNA search within sequences) (ref / manual)

 PseudoMap (ref / tutorial)    RNASNP (Predicting SNP effects on local RNA secondary structure)  RBP-Var2 (ref)

 

 SNP Resources (variation & functional annotation)

GENEPI TOOLBOX (ref)   Endeavour

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

NCBI Variation Viewer   NCBI ClinVar (ref)  NHGRI Clin Genomic DB   GeneSNPs   PharmGKB   HGMD

 Ensembl Variant Effect Predictor (VEP)     AVIA  (ref / tutorial)     wANNOVAR (tutorial)    FunSeq2 (ref)

rVarBase (ref / tutorial)   SNiPA (ref)   mQTLdb (ref)   BIOS QTL Browser (ref)

SNPnexus (guide) .. PheGenI (tutorial) .. HaploReg v4 (ref) .. HumanMine (ref) .. CoreMine

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

PredictSNP2 (ref)   ClinGen Pathogenicity Calculator (ref)

dbWGFP (ref)     RVS / Reference Variant Store (ref)     Structure PPi (ref)     GenoCanyon (ref)

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

dSysMap (ref / tutorial)

  rSNP Guide .. SNPLogic .. SPSMart (comparative frequencies)

DistiLD .. SNPEffect .. SNPfunc (ref) .. GRAIL (ref)

Haplotter   Selectome - A Database of Positive Selection   dbPSHP (ref)   GERP (ref1 / ref2)   FERRET for 1KG SNP Data Download (ref)

RVIS Genic Intolerance (ref)

 

eQTL / meQTL Resources

GTEx .. NCBI eQTL Browser .. SCAN (tutorial) .. PheGenI .. QTLminer (ref) .. eQTL Databases

eQTL Resources @ Pritchard Lab (browser) .. Blood eQTL Browser .. BIOS QTL Browser (ref) .. eQTL Catalog (NESDA/NTR) (Ref)

 mQTLdb (ref) .. e/meQTL .. reQTL (ref)

seeQTL (help / ref)   Plateletomics (Platelet transcriptomics by gender)  ImmGen eQTL Browser (mouse)   

eCAVIAR: colocalization of GWAS signals and eQTLs (ref / manual)

 

Splice Site SNPs

ssSNPTarget (ref) .. AASsites (ref) .. AS-ALPS (ref)  

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

 

Coding SNP Annotation

genome Aggregation (gnomAD) Browser (formerly ExAc Browser) (ref)

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

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

 

Cancer Somatic Mutations

 COSMIC (somatic mutations in cancer) .. COSMIC Browser .. ICGC Data Portal .. NCBI Cancer Genome Anatomy Project .. cBioPortal 

Integrative OncoGenomics Database (intOgen) (ref)   DriverDBv2 (ref, help)   OncodriveFML (ref)

 CRAVAT (ref / help)    CIViC (ref)    TCGA Clinical Explorer

TransFIC    PRISMAD (ref)   BRCA1 Circos (ref)    Cancer cell line encyclopedia (CCLE) (ref)

(See also Yang, 2015 & Raphael, 2015)

 

Gene expression (incl. cancer)

Cancer Cell Line Encyclopedia / CCLE (ref)   Human Protein Atlas: Cancer

   RNA-seq Atlas (ref)   Expression Atlas (ref)   lnCaNet Database (ref)

TSEA (Tissue Specific Expression Analysis) (ref)

 

Cancer Informatics

Cancer Genomics and Epidemiology Navigator (CGEN)

Databases for Cancer Genomics (Table 2 in Chin, 2011)

UCSC Xena Browser  

 

Epigenetics

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

Int Hum Epigenet Cons (IHEC)   IHEC Data Portal  

HEDD (Human Epigenetic Drug Database) (ref)

 

Proxy Search

ssSNPer .. SNAP .. SNPSnap (ref / guide) .. SPOT (ref / user guide) .. HaploReg v4 .. CandiSNPer (ref)  

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

 

Transcription Factor Binding Site Search

TransFac  TFBS Search (Qiagen)  TFBS Mapper (refTFBIND  MFold   JasPar  PAZAR  SNP@llincRNA TFBS (ref)

 Swiss Regulon (by TF Name)   AR Target Gene Dbase   TESS-discontinued  

CTCFBSDB v2 (ref)

 

Chromatin Features Databases

Cistrome DB (for chromatin features) (ref)   NHGRI HistoneDB v.2 (ref

Chromatin Chromatin Space Interaction (CCSI) (ref)   4D Genome (ref)

Human Histone Modification Database (HHMD) (ref)

 

GWAS Resources

 GWASdb v2    Catalog (NHGRI-EBI)   GWAS Central   HuGE GWAS Integrator

PhenoScanner (manual)    GRASP (ref / overview / user guide)    GWATCH (ref / tutorial)    GWAS3D (ref / help / manual

HaploReg v4 (ref)    RegulomeDB (GWAS)

 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)  

CAPE: CellulAr dePendent dEactivating mutations predictor (ref

GARLIC: GWAS-based Prediction Toolkit for Connecting Diseases and Cell Types (ref)  

LD Hub (ref)    easyGWAS (ref / tutorial)    HESS: Heritability Estimation from Summary Statistics of GWAS (ref)    MR-Base (ref1 / ref2)

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

PheWAS Catalog   Metabolomics GWAS    PGWAS: Proteomics GWAS (ref)

NHGRI GWAS Catalog as a Table (2015)

eCAVIAR: colocalization of GWAS signals and eQTLs (ref / manual)

 

GWAS SNP Set Analysis

i-Gsea4Gwas Web Server (ref / tutorial)    GSEA & GSEA-SNP    VSEAMS (ref)-for local use    MAGENTA (ref)-requires MatLab

 

Gene Set Enrichment and Pathway Analysis

ENRICHR (ref / help)    GSEA/MSigDB    ConsensusPath (CPdB) (ref / protocol)

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

 Cytoscape    Disease Connect    ToppGene (ref)    Panda (ref / video tutorial)

UniHi   Reactome (user guide)   BioSystems   Pathway Searcher   KEGG   PDB: Biological Process Browser

GSEA & GSEA-SNP   GIANT (Gene Networks in Tissues; Ref)   Onto-Tools (user guide)

Comparative Toxicogenomics Database (CTD) 

 

Gene Network Analysis

The Genome Network Project (GNP)   Genetic Network Analysis Tool (GNAT) (ref)

GeneNetwork-UT / GN2 (co-expression)   Human Gene Correlation Analysis (co-expression) (ref)   CORD (ref) (co-regulation) 

GIANT (Gene Networks in Tissues; ref)    BioGrid    String  

RegNetwork (TF and miRNA networks) (ref)   ChIPBase (ref)

 Genome-wide Predictions of miRNA Regulation by Transcription Factors Database  (ref)

Ingenuity Target Analysis  

 

Gene Ontology

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

GeneNetwork-UCMG (function, expression and co-expression) .. GeneNetwork-UT

 

Immunoinformatics

 MHC Haplotype Project   dbMHC (search)

IPD-IMGT/HLA (ref)    MHCcluster (ref)   Immune Epitope Database (IEDB) (video tutorials/ref)

Registry of Antibody-Defined HLA Epitopes (ref)    HLA Epitopes @ Allele Frequencies.Net (ref)

IMGT/HLA Allele Query    IGDAWG (Global Frequency Map Browser)   PyPop Population Data

 ImmPort (tutorial)   ImmVar   ImmunoBase (browser)   ImmuNet (ref)   ImmuneCellScience (ref)   ImmGene-Mouse (ref / video)

FineMapping / PICS (ref)  

BIGDAWG Case-Control HLA Data Analysis (ref)    HLA-NET GENE[RATE] Tools (publications)

 

Proteins

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

Structure PPi (ref)   Phyre 2 (ref; tutorial; tutorial notes)   Phyre 2 Investigator   ConsensusPath (CPdB)  (ref)

SusPect (ref)   UniProt (query)   SwissProt   Protein-Protein Interaction Mining Tool   MINT (interactions)

BioPlex (ref)   Genome3D   SMART   STRING

Structural Biology Knowledgebase (SBKB)  MEME Suite   iHOP

Protein Sequence Analysis

ExPasy: Proteomics Tools    Tools for Protein Analysis    GenomeNet Chemical Analysis Tools  

 Post-translational Modifications

GPS    PhosSNP (ref)    Functional Glycomics

Protein-related Bioinformatics Resources

 

Human Metabolome Database (HMDB)   Metabolomics GWAS   HumanMine (ref)

 ANNOVAR (ref / quick startup guide / protocol)  wANNOVAR (tutorial)   AVIA

AURA: Atlas of UTR Regulatory Activity (ref)

CCC analysis: CCSI (ref)    3CDB (ref)

 

Disease Databases

dSysMap (ref / tutorial)   Disease Connect   CoreMine   GWASdb v2   Phenolyzer (ref / tutorial)   PhenoPred   SNPs3D  DisGeNET (ref)

FANTOM CAT Traits Database

Comparative Toxicogenomics Database (CTD) 

 

Nature/Cell Resources  

ENCODE     Epigenome RoadMap    TCGA   IHEC

 

Various Other Resources

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) 

 

STR Database

 TaqMan SNP Genotyping Assays (1)  (2)  

Chang Bioscience Tools    VISTA Tools

ThermoFisher Learning Center .. Access Biotech

Restriction Enzyme Database .. NEBCutter .. GenScript Tools

Primer Design Resources .. SNP-RFLPing (PCR-RFLP Design)

Primer Design Software Primer3 (help) .. Primer3Plus .. BatchPrimer3 (help / ref) .. Viz-Primer

 Oligo Analyser and PrimerQuest (IDT)

FastPCR .. FastPCR Online Tools .. In Silico PCR .. OEGE Sequence Tools 

Multiple Sequence Alignment: Clustal (help) .. BioEdit .. Topali v2 .. Jabaws   

Expasy Translate Tool .. ORF Finder (NCBI) .. JustBio Bioinformatics Tools  

 

Search Templates

(use these for quick searches by changing the indicated identifier to yours in the address line)

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

GWAS Cat (rs#)   PheGenI (rs#)  dbGAP (rs#)   GWAS Central (rs#)  ImmunoBase (rs#)

 GWAS Central (Gene Name)    Ingenuity Target Explorer (Gene Name)

 GTEx (rsID)  GTeX (Gene Name)  GTEx Visualizer (Gene Name)  GTEx (your own SNP)  GTEX (alt. splicing variants for a gene)

 Variation Viewer (geneName)   Broad Institute (rs#)   rVarBase (rs#)   PhenoScanner (rs#)   HaploReg v4 (rs#)

Vega / Ensembl (Gene Name)  Ensembl (rs#)   SNPedia (rs#)

RegulomeDB (chr#/nt#)   OpenSNP (rs#)  MSV3d (missense rs#)

ENCODE Regulatory Elements DB (Gene Name)    GenCode - Alternative Splicing Variants (Gene Name)

 Expression Atlas (Gene Name)   Protein Atlas (Gene Name)   

COSMIC Gene Analysis Search Template (by Gene Name)

LnCaNet search: general info by Gene ID; expression by Gene ID; PTM by Gene ID

mirBase microRNA search (Chr coordinates)

Qiagen/SABiosciences TFBS search:  Gene Name / TF name

 HGMD (Gene Name)   PPI Mining Tool (Gene Name)    GeneCards    Entrez Structure   RVIS (GeneName)  

Amino Acids   Genetic Code   Ambiguity (Mixed Base) Codes

 BioCompare

 

ONLINE TUTORIALS / TRAINING

EMBER - A Practical Guide to Bioinformatics

GOBLET - the Global Organisation for Bioinformatics Learning, Education & Training

Applied Bioinformatics Course (ABC) (ref)

Bioinformatics Training and Services (BITS) - Exercises

Tutorials: NCBI  Ensembl  UCSC  Haploview  Galaxy  GoldenHelix  ImmPort  Omixon

EMBL-EBI Training

Tutorials @ Open Helix    Open Helix Blog    Mayo Bioinfo YouTube Channel

Online Lectures on Bioinformatics

Getting Genetics Done   BioStars   Swedish Bioinformatics Support (SBS)

Genome Biology & Applied Bioinformatics Course Notes

 

LINKS

Links to Bioinformatics Tools @ ABC

Bioinformatics.ca

OMICSTools

Online Bioinformatics Resources Collection

 

Mehmet Tevfik DORAK, M.D., Ph.D.

 

HLA     MHC    Genetics     Evolution     Biostatistics     Population Genetics    Genetic Epidemiology    Homepage

 

17 July 2017