biological databases exercises. discovery of distinct sequence databases using ensembl

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Biological databases Exercises

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Page 1: Biological databases Exercises. Discovery of distinct sequence databases using ensembl

Biological databases

Exercises

Page 2: Biological databases Exercises. Discovery of distinct sequence databases using ensembl

• Discovery of distinct sequence databases using ensembl

Page 3: Biological databases Exercises. Discovery of distinct sequence databases using ensembl
Page 4: Biological databases Exercises. Discovery of distinct sequence databases using ensembl
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• View the genomic context

Page 8: Biological databases Exercises. Discovery of distinct sequence databases using ensembl
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• Try some links to other databases

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HUGO ID genecards

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REFSEQ

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Swissprot

Page 17: Biological databases Exercises. Discovery of distinct sequence databases using ensembl

• Try some interesting databases at the NCBI site

• locus link

• Pubmed database

• DDD database

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ID accessionnumber of a genomic sequence in the nucleotide database

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ID accessionnumber of a mRNA in the nucleotide database

Page 26: Biological databases Exercises. Discovery of distinct sequence databases using ensembl

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

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Reference to protein database

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• Some other interesting sites at ncbi– EST database– UniGENE database– DDD– Microbial genomes database

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ICES 2006 (updated 01102006)

(nieuwe release ensembl)

Page 34: Biological databases Exercises. Discovery of distinct sequence databases using ensembl
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How many microbial genomes have been fully sequenced

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How many plant species have been fully sequenced

Page 38: Biological databases Exercises. Discovery of distinct sequence databases using ensembl

Can you find the mammoth sequencing project

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Search for the genomic map of the Chimp using the genome biology link

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Check out RefSeq

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To update the gene database

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2 splice variants

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• Redundant database

• GenBank

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Ensembl

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Genomic location

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Evidence used to annotate

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Different transcripts

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Links to related databases