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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 – 9-12am Feb. 2 Rm 100 Radiology – Computer lab 10:15-12:15 Feb. 3 – Three other labs available 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. Major components of NCBI • • • • • • GenBank PubMed Entrez BLAST Cluster of orthologous groups OMIM GenBank • Database of DNA and protein sequences • Searchable • Caution: Sequences deposited by the community, not curated for accuracy. PubMed • Database of all scientific journal articles. • PubMed Central - free access to thousand of these articles. • Many articles are available electronically through MSU libraries. BLAST • Basic Local Alignment Search Tool • Comparing nucleotide sequences and protein sequences • Microbial specific BLAST page OMIM • Online Mendelian Inheritance in Man. • Database that links diseases and genes TIGR • Comprehensive microbial resource (CMR). • Many genomes. • Tools to analyze genomes. 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 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. 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. 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