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Exploring Genome Tools and Databases for Microbial Analysis

Learn about microbial genome databases and tools for analysis. Access NCBI, GenBank, PubMed, BLAST, and more. Class details available at http://www.msu.edu/~rbritton.

jacquelinebrown
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Exploring Genome Tools and Databases for Microbial 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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