GENBANK, SWISSPROT AND OTHERS

1
GENBANK, SWISSPROT AND OTHERS

• As Problem Sources for CSE 549
• Andriy Tovkach
• Genetics

2
GENBANK OVERVIEW

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

3
FILE FORMAT

• Header
• Features
• Sequence
• (see files)

4
FASTA FORMAT

• Single line description begins with gt
• Followed by sequence data
• Can be both protein or DNA

5
ENTREZ as RETRIEVAL SYSTEM

• PubMed 12 million citations from life science
  journals
• Nucleotide collection of DNA sequences
• Protein protein sequences from SwissProt
• Genome genomes of over 800 organisms
• Also Structure, PopSet, Taxonomy, OMIM

6
PROTEIN DATABASES

• SWISS-PROT
• EBI TREMBL
• NCBI GENPEPT (already in history)

7
GENOME DATABASES

• SGD
• homepage
• example 1.1
• example 1.2
• Wormbase
• Ensembl Human Genome Browser

8
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
• Thats why computer scientists are welcome in
  biology

9
LITERATURE

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