HLA     MHC    Genetics     Evolution     Biostatistics     Population Genetics    Genetic Epidemiology    Homepage

 

BIOINFORMATICS TOOLS

(for Genetic Epidemiologists)

Mehmet Tevfik DORAK, MD PhD

 

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 (2016)Web Server Issue (2015);  Database: Biomart IssueEnsembl Issue

 

Nucleic Acids Research Databases Catalog

 

Societies

ISCB     ISMB

 

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 (tutorial)   SPS 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)   NGSmethDB (ref)

HapMap Genome Browser   1KG (Browser - Quick Start Guide)-(NCBI)   UK10K (ref)   GENCODE Browser   VaDE   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 (HaemAtlas)    T1Dbase 

 

 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)   NHGRI Histone Database (ref

Genomic coordinate conversion: Ensembl Assembly Converter   Kaviar

 

ncRNA (microRNA/lncRNA) & Pseudogene Resources

 miRBase  miRDB  mrSNP  TargetScan  dPORE-miRNA  miREnvironment  StarBase (tutorial / 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)

lncRNA and Disease Database   ncRNA Databases Resource (NRDR)  

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    LncDisease (ref)  

miRNA-SNP db (ref)   AVIA miR SNP Analysis Tool  lncRNA-SNP db (ref)   LincSNP v2.0 (ref)   lncRNASNP (ref)

NONCODE (ref)   NPInter v3 (ref)

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

 PseudoMap (ref / tutorial)   lnCaNet Database (lncRNA co-expression database) (ref)   co-lncRNA (ref

miTranscriptome (ref)

 

 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)    LOVD (ref)

NCBI Variation Viewer   NCBI ClinVar (ref)  NHGRI Clin Genomic DB   SNP500 Cancer   GeneSNPs   PharmGKB   HGMD

 Ensembl Variant Effect Predictor (VEP)  PupaSuite (help, tutorial, exercises)  AVIA  (ref / tutorial)

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)

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

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

dSysMap (ref / tutorial)

  rSNP Guide .. 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)   FERRET for 1KG SNP Data Download (ref)

RVIS Genic Intolerance (ref)

 

Splice Site SNPs

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

 

Coding SNP Annotation

SNPs3D .. dbNSFP (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)    Cancer cell line encyclopedia (CCLE) (ref)

(See also Yang, 2015 & Raphael, 2015)

 

Gene expression in Cancer

Cancer Cell Line Encyclopedia / CCLE (ref)   RNA-seq Atlas (ref)   Expression Atlas (ref)   lnCaNet Database (ref)

 

eQTL / meQTL Resources

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

eQTL Resources @ Pritchard Lab (browser) .. Blood eQTL Browser .. BIOS QTL Browser (ref) .. mQTLdb (ref) .. m/meQTL .. reQTL (ref)

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

Plateletomics (Platelet transcriptomics by gender)

 

Proxy Search

ssSNPer .. SNAP .. SNPSnap (ref / guide) .. GLIDERS .. SPOT (ref / user guide) .. HaploReg v4 .. 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 (refTFBIND  MFold (Basic)  JasPar  PAZAR  SNP@llincRNA TFBS (ref)

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

 

GWAS Resources

 GWASdb v2    Catalog (NHGRI-EBI)   dbGAP Association Results Browser   GWAS Central   HuGE GWAS Integrator   Database (Japan) 

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

PheWAS Catalog   Metabolomics GWAS

NHGRI GWAS Catalog as a Table (2015)

 

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

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

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

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)   Onto-Tools (user guide)

 

Gene Network Analysis

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

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

GIANT (Gene Networks in Tissues; ref)    BioGrid    String

Ingenuity Target Analysis

 

Gene Ontology

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

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

 

Immunoinformatics

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

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

 ImmPort    ImmVar    ImmunoBase (browser)   T1Dbase (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   

 PMut (ref)   SusPect (ref)

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

 Genome3D  SMART  STRING

Structural Biology Knowledgebase (SBKB)  MEME Suite  

Protein Sequence Analysis

 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)

 

Nature Resources  

ENCODE     Epigenome RoadMap    TCGA

 

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) 

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

STR Database

 TaqMan SNP Genotyping Assays (1)  (2)  

Chang Bioscience Tools    VISTA Tools

HIV Databases

Ambion Technical Library .. Access Biotech

Restriction Enzyme Database .. Blast REbase .. NEBCutter

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: ClustalW (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#)  1KG (rs#)  Ensembl (rs#)

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

 GWAS Central (Gene Name)   T1Dbase (Gene ID)   Ingenuity Target Explorer (Gene Name)

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

 Variation Viewer (geneName)   Broad Institute (rs#)   VaDE (rs#)   rVarBase (rs#)   PhenoScanner (rs#)   HaploReg v4 (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#)  OpenSNP (rs#)  MSV3d (missense rs#)

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

HaemAtlasView Expression Levels (Gene Name)   Expression Atlas (Gene Name)   Protein Atlas (Gene Name)   Blueprint (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      SwissRegulon TFBS search (TF 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)

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

 

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

 

HLA     MHC    Genetics     Evolution     Biostatistics     Population Genetics    Genetic Epidemiology    Homepage

 

4 November 2016