Genetics Education

Content

Agenda

Information

Faculty

Click here to see an interview with workshop organizer, Dr. Simon Gregory.

The 2007 DBW was featured on NPR by WUNC's Rose Hoban. C lick here to listen to the report.

Bioinformatics Workshop Modules

2009 Introduction

Module 1: De novoAnnotation and Analysis of Sequence

• Module 1 Introduction
• EBI Homepage
• NCBI Homepage
• ENTREZ
• NCBI BLAST
• EBI Blast Server
• Sanger Institute Blast Server
• VEGA Vertebrate Genome Annotation Database
• PSI-BLAST
• ORF Finder
• SPIDEY
• SIM4
• EST2GENOME
• ClustalW
• ClustalW at EMBnet
• GeneDoc

   Promoter Prediction Programs:

• FirstEF
• Eponine
• Dragon Genome Explorer
• Promoter Scan
• TFsearch
• Genomatix Suite

Module Files
Genome Graphs

Modules 2 and 3: Genome Browsing

• Module 2 Introduction
• Module 3 Introduction
• Genome Browser at UCSC
• Ensembl Browser
• EBI Homepage
• NCBI Homepage
• Map Viewer
• UCSC Table Browser
• UCSC BLAT Server
• ENCODE Project
• BioMart
• VEGA Vertebrate Genome Annotation Database
• EBI Blast Server
• Sanger Institute Blast Server
• NCBI BLAST Server

Module 4: Comparative Genomics

• Module 4 Introduction
• Ensembl Browser
• Genome Browser at UCSC
• Decode

Module 5: Exploring Gene Function and Disease

• Module 5 Introduction
• Entrez
• OMIM
• UniGene
• HGMD
• InterPro
• Go
• KEGG
• GeoProfiles
• Polyphen
• COSMIC
• DECIPHER
• RFAM
• MiRBase

Module 6: Exploring Protein Function and Disease

• Module 6 Introduction
• PFAM
• PDB
• PDBsum
• Swissmodel
• IntAct
• InterPro
• CDD
• MSD
• JPRED
• DeepView
• Copy Number Variation Database

Module 7: Introduction to Sequence Variation

• Module 7 Introduction
• Exoseq
• dbSNP
• HGVBase
• Ensembl
• HapMap

Module 8: Working with the Genome Browsers

Module 9: Working with Sequence Variation

• Ensembl
• HapMap
• Haploview
• dbGAP
• FastSNP

Module Files
Genotype Data (.ped)
SNP Locations (.info)

Module 10: The State of 21st Century Genomic Technologies

• Module 10 Introduction

Module 11: Major Bioinformatic Resources

• Module 11 Introduction
• Ensembl
• NCBI Homepage
• OMIM
• MGI
• ZFIN
• Flybase
• OMIA
• BioGPS

Module 12: Introduction to Expression Microarrays

• Microarray Introduction
• Choosing a Microarray Platform
• Sample Variation
• RNA Quality
• RNA Isolation Techniques
• Pooling Samples
• Replicates
• Agilent arrays
• Affymetrix arrays
• Illiumina arrays
• Homebrew arrays
• Agilent's GeneSpring GX 10.0
• Partek
• PAM
• Bioconductor
• MetaCore

   PDFs:

• GeneSpring GX Quick Start Guide
• GeneSpring v10 Manual
• MetaCore Systems Manual
• Partek Documentation
• Expression Console 3prime Expression Quickstart Guide
• Expression Console Exon Level Quickstart Guide
• Expression Console Gene Level Quickstart Guide
• Expression Console How to Export with Annotations

Module 13: Microarray Analysis

• Module 13 Introduction
• Ingenuity
• Genomic Health
• Enbrez Gene
• Oncomine
• Adobe
• Ensembl

Module Files
Microarry Files
References

Module 14: Expression Pathway Analysis

• Module 14 Introduction
• KEGG
• Gene Ontology
• Reactome
• Pathway Interaction Database
• Pathguide
• EntrezGene
• DAVID Bioinformatics Resource
• Ingenuity
• DiRE

Module 15: Proteomics

• Module 15 Introduction
• Mascot
• MS-Tag
• Omssa
• PepFrag (Prowl)
• pFind
• Phenyx
• Sonar (Knexus)
• X!Tandem (The GPM)
• XProteo
• Matrix Scicence
• Peptide DB
• Uniprot