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)

Genome Browsers:

 UCSC Human Genome BioInformatics   

Ensembl Genome Browser (Human) .. Vega Genome Browser (Human) .. NCBI Epigenomics (Help) / Browser

HapMap Genome Browser   1KG (Browser)-(NCBI)  

CNV Browser   eQTL Browser   NextBio 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) .. COSMIC (somatic mutations in cancer) .. ICGC .. NCBI Cancer Genome Anatomy Project   

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)

 

microRNA Resources

 miRBase  miRDB  mrSNP  TargetScan  dPORE-miRNA  miREnvironment  StarBase  microSNiPer (ref)

 Human miRNA Disease Database (HMDD)   miRCancer   OncomiRDB (ref)   HOCTAR (ref)

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

 NHGRI Histone Database 

 

SNP Resources

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

Links to Gene Prioritization Tools

NCBI Variation Viewer   NHGRI Clinical Genomic Database   Ensembl Variant Effect Predictor

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

GVS .. PERLEGEN .. UCSC .. ToppGene .. Br1958BC .. ssSNPer .. SNAP .. GLIDERS .. SPOT (ref / user guide)

F-SNP .. RegulomeDB (GWAS) .. SNPexpress .. SNPxGE2   

eQTL Resources @ Pritchard Lab (browser) .. GTEx .. SCAN (tutorial) .. seeQTL .. Genevar .. PhenGenI (tutorial) .. SNPexp

dbSNP .. dbSNP Tutorial .. SNP500 Cancer .. HGBASE .. HGMD .. HaploReg (ref) .. CandiSNPer (ref) .. dbSTEP (ref)

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

 GeneSNPs .. rSNP Guide .. SNPEffect .. SNPLogic .. SNP@Ethnos .. SNPranker (ref) .. PharmGKB

Haplotter   Selectome - A Database of Positive Selection

 DistiLD .. stSNP .. MutDB .. SiPEP .. VaryGene .. Gene Prospector (ref)

SNPs3D .. PolyPhen-2 .. SIFT (by SNP ID) .. PolyDoms  

SNPtagger .. SNP HaploTag Calculator .. HaploBlockFinder

 Panther (Download) .. Pmut .. PupaSuite (Help, Tutorial, Exercises) .. SNP Imputability

Genomic Confounding Browser (ref)

Software and Databases for SNP Research

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

 TaqMan SNP Genotyping Assays    Affymetrix

 

GWAS Resources

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

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

OMICtools   LocusZoom (Ref)

 

Gene Set/Network Analysis

DAVID (ref / tutorial) .. PANOGA (ref / tutorial) .. See also Huang et al, 2009

 Cytoscape    Disease Connect

UniHi .. Reactome .. BioCarta .. GeneMAPP (Gene Pathway Profiler) (tutorial)

BioSystems    Pathway Searcher    KEGG    PDB: Biological Process Browser

GSEA & GSEA-SNP

 

Gene Ontology

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

 

 Gene Regulation Databases   Plateletomics (Platelet Transcriptomics by Gender)

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

Transcription Element Search Software (TESS)

Searching TF Binding Sites   TransFac    MFold  (Basic)   Mapper   JasPar

PatSearch   UniProt / SwissProt

STR Database

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 (free) .. 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

 

Search Templates

Gene (Gene Name1/Human)  Gene (GeneName2)  Gene (GeneID)  dbSNP (GeneID)  dbSNP (rs#)  NextBio (rs#)  GWAS Cat (rs#) 

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

 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

Tutorials @ Open Helix

Online Lectures on Bioinformatics

 

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

 

9 December 2014