biological databases exercises. discovery of distinct sequence databases using ensembl
TRANSCRIPT
Biological databases
Exercises
• Discovery of distinct sequence databases using ensembl
• View the genomic context
• Try some links to other databases
HUGO ID genecards
REFSEQ
Swissprot
• Try some interesting databases at the NCBI site
• locus link
• Pubmed database
• DDD database
ID accessionnumber of a genomic sequence in the nucleotide database
ID accessionnumber of a mRNA in the nucleotide database
Name of the coding sequenceID of the protein in the protein database (REFSEQ)Crossreferences to the corresponding entry in the nucleotide database and to locuslink
Zoom in on a particular gene
Location of the gene
Reference to protein database
• Some other interesting sites at ncbi– EST database– UniGENE database– DDD– Microbial genomes database
ICES 2006 (updated 01102006)
(nieuwe release ensembl)
How many microbial genomes have been fully sequenced
How many plant species have been fully sequenced
Can you find the mammoth sequencing project
Search for the genomic map of the Chimp using the genome biology link
Check out RefSeq
To update the gene database
2 splice variants
• Redundant database
• GenBank
Ensembl
Genomic location
Evidence used to annotate
Different transcripts
Links to related databases