BIO341 Gene Discovery Section 2 Practical Genome Projects

1
BIO341 - Gene DiscoverySection 2
PracticalGenome Projects

• Jasper Rees
• Department of Biochemistry, UWC
• www.biotechnology.uwc.ac.za/teaching/BIO341

2
Objectives

• To select a species for which a genome project is
  in progress
• To use Internet resources to locate information
  about genome projects generally
• To locate resources relating to the chosen
  species specifically
• To write a 2 page review of the specific genome
  project, discussing the scientific interest in
  the organism, and the nature of the genome
  project
• To publish the review on the BIO341 web page

3
National Biotechnology Information Centre

• At the National Library of Medicine, Washington
  DC, USA
• Publicly funded for free access to everyone
• Site for DNA sequence database (Genbank)
• Site for biomedical research literature database
  (PubMed) and free journals (PubMed Central)
• Site for protein and structure databases
• Site for Human genome data
• Site for database searching (BLAST)

4
DNA Databases at NCBI

• Genbank All submitted DNA sequences, published
  and unpublished, except ESTs. All published DNA
  sequences go to Genbank
• dbEST EST sequences from all public EST
  projects, including human and mouse
• Human, Drosophila, yeast, genome databases
• Smaller databases of specific classes of
  sequences
• Seachable with BLAST

5
Genome databases elsewhere

• TAIR Arabidopsis
• Yeast
• All searchable with BLAST

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Protein Databases at NCBI

• nr non-redundant database all submitted
  protein sequences, both characterised and
  predicted
• Swissprot curated and annotated protein sequence
  database
• Kabat sequences of immunological interest
• Yeast all yeast predicted and known proteins
• Searchable with BLAST

7
Structure Database at NCBI

• All released protein structures (generally one
  year after publication)
• NMR and X-ray crystallography data
• Searchable for text or sequence (BLAST), not for
  structure
• Need other servers for structure similarity
  searching

8
PubMed Research Papers Database at the NCBI

• PubMed, covers biomedical research papers,
  covering medicine, biology, and some plant
  journals.
• Searchable
• Fully internally indexed to allow search for
  related articles
• Linked to journal web sites

9
PubMed Central

• Archive of research literature available free
  from the NCBI
• Only some journals at present.

10
Nature Genome Gateway

• Set of original research papers relating to
  genome research published in Nature Genome
  Gateway
• Human genome specific section
• Freely available

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Science Genome Landmark

• Free papers from the journal Science

12
Other genome resources

• Demeters Genomes
• Stanford Genome Resources

13
Genome Projects - species list

• Human
• Mouse
• Rat
• Drosophila
• C.elegans
• Saccharomyces
• E.coli
• Helicobacter
• Tetraodon
• Danio rerio

• Ara.bidopsis
• Medicago
• Wheat
• Barley
• Maize
• Rice
• Sorghum
• Pine
• Poplar
• Tomato
• Dictyostelium

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Internet search engines

• Search engines that index Web sites
• Cover about 15 of the Internet at most, not all
  sites are indexed.
• Altavista.com
• Google.com
• Excite.com
• Yahoo.com