Genome databases and webtools for genome analysis Become

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 -12 am 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 • • • Gen. Bank Pub. Med Entrez BLAST Cluster of orthologous groups OMIM

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

Pub. Med • Database of all scientific journal articles. • Pub. Med 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.

Subti. List • 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