Biological databases Exercises. Discovery of distinct sequence databases using ensembl.

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