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Genome databases and webtools for genome analysis

Genome databases and webtools for genome analysis. Become familiar with microbial genome databases Use some of the tools useful for analyzing genome Visit sites used in lab exercise. Web address for class. http://www.msu.edu/~rbritton Can also access through MMG webpage NCBI training

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Genome databases and webtools for genome analysis

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  1. Genome databases and webtools for genome analysis • Become familiar with microbial genome databases • Use some of the tools useful for analyzing genome • Visit sites used in lab exercise

  2. Web address for class • http://www.msu.edu/~rbritton • Can also access through MMG webpage • NCBI training • 9-12am Feb. 2 Rm 100 Radiology • Computer lab 10:15-12:15 Feb. 3 • Three other labs available

  3. NCBI • National Center for Biotechnology Information • Most comprehensive resource for genomic, computational, and literature information on the internet. • If you pursue a career in biology, you will get to know NCBI very well.

  4. Major components of NCBI • GenBank • PubMed • Entrez • BLAST • Cluster of orthologous groups • OMIM

  5. GenBank • Database of DNA and protein sequences • Searchable • Caution: Sequences deposited by the community, not curated for accuracy.

  6. PubMed • Database of all scientific journal articles. • PubMed Central - free access to thousand of these articles. • Many articles are available electronically through MSU libraries.

  7. BLAST • Basic Local Alignment Search Tool • Comparing nucleotide sequences and protein sequences • Microbial specific BLAST page

  8. OMIM • Online Mendelian Inheritance in Man. • Database that links diseases and genes

  9. TIGR • Comprehensive microbial resource (CMR). • Many genomes. • Tools to analyze genomes.

  10. SubtiList • Website for B. subtilis genome. • Features • Annotated genes • Gene region display • Updated BLAST searches • BLAST and pattern search capabilities • Links to journal articles and protein databases

  11. RDP • Ribosomal database project • Curated at MSU • Contains a compilation of all ribosomal DNA sequences • Second database contains information regarding copy number of ribosomal RNA.

  12. KEGG • Kyoto Encyclopedia of Genes and Genomes • Often changing database of gene content, metabolic pathways, etc. • Excellent resource for reconstructing pathway in organism of interest.

  13. Conclusions • GOOD: A LOT OF USEFUL INFORMATION/RESOURCES TO VISUALIZE DATA. • BAD: A LOT OF NOT SO USEFUL INFORMATION/RESOURCES TO VISUALIZE DATA. • UGLY: SOME OF THE ATTEMPTS TO PUT INFORMATION ON THE WEB

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