Working with the Human Genome Sequence

Topics
Sequence Formats and Retrieval:
DNA databases: Embl, Genbank, DDBJ
Protein databases: Uniprot
Entrez - seach sequence information, including Refseq BLAST

Genome Browsing:
Ensembl - full coverage including BioMart
VEGA
UCSC

De novo analysis of Sequence:
VEGA
DNA analysis - ORF finder
Alignment of splicing cDNA to genomic DNA - Spidey, Est2genome, SIM4
Multiple Sequence Alignment - CLUSTALW
Alignment viewing and Editing- Jalview, GeneDoc

Exploring Function and Disease:
Understanding Protein Function - from domains to structure (covering Pfam, InterPro, TreeFam CDD, CATH, SCOP, PDB, MSD)
Proteins as part of functional networks - iPfam, IntAct
Secondary Structure predictions
Disease databases COSMIC, OMIM, DECIPHER
Mapping disease associated SNPs to Proteins - Polyphen, SNPs 3D Rfam and microRNAs (miRBase)

Sequence Variation:
Ensembl SNP information, Geneview in dbSNP
Glovar, JSNP, HGVBase
Genotyping
Haplotypes and HapMap
Haploview

Comparative Sequence Analysis:
Homologous gene identification - Paralogues and Orthologues
Ensembl - orthologue prediction, MultiContigView
EntrezGene - BLink, Homologene
Comparative Genome Analysis - UCSC, Zpicture, VISTA

The course is subsidised by the Wellcome Trust for scientists based in academic institutions anywhere in the world.