Genetics Education

Agenda

Dates and Location

Contact

Cost

Faculty

Links and Files

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

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

Links and Files

Welcome

Module 1: Manual Genome Annotation and de novo Analysis of Sequence
Module 1 Introduction
NCBI BLAST
ORF Finder
SPIDEY
SRS
EBI Homepage
InterPro
ENTREZ

Links for Module 1:
SRS at EBI
ClustalW
Vega

Module 2: Genome browsing
Module 2 Introduction
Map Viewer
Ensembl
Human Genome Browser
Human Genome Browser (mirror)
Integrative Genomics Viewer

Module 3: Comparative genomics
Module 3 Introduction
NCBI Entrez
Entrez Gene
Ensembl
Approved Sequencing Targets and level of coverage proposed/completed
International Sequencing Consortium
NCBI Trace Archive BLAST search
Ensembl Trace BLAST search
Integrated Protein Informatics Resource for Genomic and Proteomic Research
Constructing Phylogenetic Trees
MEGA
MrBAYES
GARLI
Phylip
TreeView X
UCSC
ZPicture
VISTA
A Compilation of Useful Websites
Primer3 for primer design
ClustalW
DIALIGN
MUSCLE
MacClade
HyPhy
ECR Browser
PipMaker
RepeatMasker
BCM SearchLauncher

Reference:  Wheeler, D. L., D. M. Church, et al. (2003). "Database resources of the National Center for Biotechnology." Nucleic Acids Res 31(1): 28-33.

Module 4: Introduction to sequence variation
Module 4 Introduction
dbSNP
JSNP
HGVBase
Sequence retrieval server (SRS)
Illumina
Affymetrix
HapMap
Ensembl

Module 5: Working with sequence variation
Ensembl
OMIM
Entrez
dbSNP
HapMap
Haploview

Module 6: Exploring gene function and disease
Module 6 Introduction
Pfam
InterPro
InterProScan
CDD
PDB
MSD
PDBsum
SWISS-MODEL
JPRED
IntAct
OMIM
Cosmic
KEGG
DECIPHER
Polyphen
Rfam
MiRBase

Module 7: Introduction to microarrays


Module 8: Genomic arrays
Module 8 Introduction
CAPWEB
VAMP
Clone Locations
GBMS File
Expression Crossover
Filtered DNA Methylation Raw Values

Module 9: Expression arrays
Module 9 Introduction
Affy Expression CEL files (zip file)
GeneSpring GX 9 Quick Start Guide
Partek Tutorial, part 1
Partek Tutorial, part 2
Expression Consol Quickstart Guide
IPA 6 Help Manual

Module 10: Analytic approaches and applications to microarrays
Module 10 Introduction
References for Module 10
Expression Analysis References
Directions for Expression Practical
Data files

Software
GeneDoc     (PC only)
Cn3D(PC & Mac)
Haploview (PC & Mac)
Deep View (PC & Mac)

Downloads
Genotype Data (.ped)
Phylip (.phylip)
SNP Locations (.info)
Q9UBS5
Genome Graphs