Transcript Lecture_2

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
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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
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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