GENBANK, SWISSPROT AND OTHERS As Problem Sources for CSE 549 Andriy Tovkach Genetics.

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Presentation transcript:

GENBANK, SWISSPROT AND OTHERS As Problem Sources for CSE 549 Andriy Tovkach Genetics

GENBANK OVERVIEW  Consists of EMBL, NCBI and DDBJ  Started 10 years ago  Exponential growth (graph)graph  On Saturday, the 7 th – 20.2 billion bases

FILE FORMAT  Header  Features  Sequence (see files)see files

FASTA FORMAT  Single line description begins with >  Followed by sequence data  Can be both protein or DNA

ENTREZ as RETRIEVAL SYSTEM  PubMed – 12 million citations from life science journals  Nucleotide – collection of DNA sequences Nucleotide  Protein – protein sequences from SwissProt Protein  Genome – genomes of over 800 organisms  Also Structure, PopSet, Taxonomy, OMIM

PROTEIN DATABASES  SWISS-PROT SWISS-PROT  EBI – TREMBL  NCBI – GENPEPT (already in history)GENPEPT

GENOME DATABASES  SGD: homepage example 1.1 example 1.2  Wormbase Wormbase  Ensembl Human Genome Browser Ensembl Human Genome Browser

CONCLUSIONS  Sequencing projects produce a lot of data  These data have at least to be structured in the databases  Ideally all sequences need high-quality human annotation  That’s why computer scientists are welcome in biology

LITERATURE  Genebank presentation by Manpreet Katari (CSE 549, Fall 2000)  Thomas Lengauer (Ed.) Bioinformatics – From Genomes to Drugs  Entrez website  Google