Cold Spring Harbor Laboratory, Cold Spring Harbor, New York USA
November 18-19, 2008
The Genome Access Course is an intensive two-day introduction to bioinformatics. The course is broken into modules that are each designed to give a broad overview of a given topic, with ample time for examples chosen by the instructors. Each module features a brief lecture describing the theory, methods and tools followed by a set of worked examples that students complete. Students are encouraged to engage instructors during the course with specific tasks or problems that pertain to their own research.
The core of the course is the analysis of sequence information framed in the context of completed genome sequences. Featured resources and examples primarily come from mammalian species, but concepts can be applied to any species. The course also features methods to assist the analysis and prioritization of gene lists from large scale microarray gene expression and proteomics experiments.
A summary of the topics are listed below: Sequence Resources and Databases
Extracting information from ENTREZ and other repositories
Sequence formats, including multiple sequence formats
Sequence conversion – using PISE
NCBI Entrez Gene, GenBank and other databases
NCBI RefSeq – Reference sequences
NCBI features such as LinkOut and BLink
NCBI TaxBrowser – Taxonomic information
Ensembl BioMart – bulk sequence and information retrieval
Model Organism Databases – e.g. Mouse Genome Informatics, Rat Genome Database, FlyBase
Expasy resources – SWISS-PROT
PANTHER
OMIM and human disease information
JCVI resources Genome Browsers
Overview of major genome browsers: Ensembl, UCSC and NCBI Map Viewer browsers
Compare content of major browsers
Adding custom tracks
de novo Analysis of Sequences
Pairwise and Multiple Sequence Alignments
Methods: Dot Matrix Analysis; Dynamic Programming; k-tuple Methods
Comparing sequences directly using blast2sequences
Understanding BLAST and BLAT searches
Scoring Matrices: PAM, BLOSUM
Iterative profile and pattern searches: PSI-BLAST, PHI-BLAST
Multiple sequence alignment programs: CLUSTALW, T-Coffee
Visualizing & editing multiple alignments
Sequence Polymorphisms
SNPs – SNP Consortium
Genotyping
Haplotypes & HapMap
Haploview
Entrez dbSNP & Genome Browsers
HGVbase
Genome Analysis
Finding functionally important units in genome sequence by comparing genomes
Ortholog and paralog prediction at NCBI and Ensembl
Multicontigview in Ensembl
Comparison tracks in the UCSC Genome Browser
DCODE Resources: The ECR Genome Browser, zPicture and rVista
Jim Watson's Genome
Protein Function and Disease
Interrogating interlinked databases for protein function and associated disease-relevant information
Entrez at NCBI: Unigene and Homologene
Interpro at EBI
Organism-specific databases: OMIM (Human), MGI (Mouse), ZFIN (Zebrafish), FlyBase (Drosophila)
The Gene Ontology Consortium
Protein Structure
Protein Data Bank 3D structure database
DeepView structure viewer
NCBI Entrez Structure
Molecular Modeling Database - MMDB
Conserved Domain Database - CDD
Cn3D - NCBI structure viewer
Structure Comparison using VAST and DALI
Fold Classification with FSSP
Catalog of Membrane Protein Structures
Catalytic Site Atlas
Gene Set Enrichment and Pathways Analysis
Prioritize genes from microarray or proteomics experiments
Gene set enrichment analysis tools – GSEA and DAVID
Pathway resources – Reactome, HPRD NetPath, KEGG
Protein interaction resources –MIPS, MINT, BIND, DIP
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