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BIOINFORMATICS TOOLS

Mehmet Tevfik DORAK

 

EMBER - A Practical Guide to Bioinformatics

USCS Human Genome BioInformatics    Galaxy (101 - Support)   ExPASy Bioinformatics Resource Portal (ref)

NCBI Global Search   GoPubMed  HuGE  LabMeeting   NCBI Tutorials   NIH Helix   NCBI Tools for Data Mining

Gene .. GeneMap .. GenAtlas .. GenCanVas .. GeneLynx .. iHOP .. ExPASy

NCBI .. BLAST .. e-PCR .. In Silico PCR .. GeneNote .. GeneCards .. GeneLoc .. CGAP-GAI

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

ENCODE    GENCODE    RegulomeDB    HaploReg    FANTOM (Papers / Software)

HapMap   HapMap Genome Browser-B36 (2008) (2009) (2010)   1KG (Browser)

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

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

Gene Exp Omnibus -GEO (NCBI) .. NCBI dbGaP  .. DAVID .. ArrayExpress (EBI)

GeneMAPP (Gene Pathway Profiler) .. NetAffX .. Gene Exp Atlas

Gene Prediction Tools:  GeneMark   AUGUSTUS Gene Prediction Tool (Tutorial)

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

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

 SOURCE (genomics tool) .. COSMIC (somatic mutations in cancer)

 miRBase   dPORE-miRNA  miREnvironment  Human miRNA Disease Database (HMDD)  lncRNA and Disease Database

 ncRNA Databases Resource (NRDR)  NHGRI Histone Database 

Comparative Toxicogenomics Database (CTD)     NIEHS SNPs   

 

SNP Resources

GENEPI TOOLBOX

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

GVS .. PERLEGEN .. USCS .. ToppGene .. Br1958BC .. SNAP .. GLIDERS

F-SNP .. RegulomeDB (GWAS) .. GTEx (Search) .. SCAN .. SNPexpress .. SNPxGE2 .. seeQTL .. Genevar .. PhenGenI

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

Haplotter   Selectome - A Database of Positive Selection

 FastSNP .. FastSNP Novel SNP Analysis .. stSNP .. MutDB .. SiPEP .. VaryGene .. QuickGO (ontology)

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

SNPtagger .. SNP HaploTag Calculator .. HaploBlockFinder

STR Database

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

Software and Databases for SNP Research

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

 TaqMan SNP Genotyping Assays    Affymetrix & Quick Query

WGAviewer  (Ge, 2008; Workshop Notes)

GWAS:

 GWASdb    Catalog (NIH)   dbGAP Association Results Browser   Database (Japan)   Johnson & O'Donnell, 2009    GWASCentral

Gene Regulation Databases 

Transcription Element Search Software (TESS)

Searching TF Binding Sites   TransFac    MFold  (Basic)   Mapper   JasPar

PatSearch   UniProt / SwissProt

NCBI Cancer Genome Anatomy Project    Pathway Searcher    KEGG

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 .. JustBio Bioinformatics

ORF Finder (NCBI) .. Tools for Data Mining (NCBI) .. NCBI Site Map

MHC Gene Table (Sanger)    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#)

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

dbSTEP (chr#; nt#)

Correlated SNPs (Br1958BC)

ABI TaqMan (Gene)

 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

Tutorials: NCBI  Ensembl  Haploview  Galaxy  GoldenHelix  ImmPort

Tutorials @ Open Helix

 

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

 

24 April 2014