Genomics, Proteomics, and Bioinformatics. Biology 224 Instructor: Tom Peavy August 31, 2009. What is bioinformatics?. Interface of biology and computers Analysis of genomes, genes, mRNA and proteins using computer algorithms and computer databases. What is Genomics?.
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Instructor: Tom Peavy
August 31, 2009
What is Proteomics?
What is the Transcriptome?
“Science is about building causal relations between natural phenomena (for instance, between a mutation in a gene and a disease). The development of instruments to increase our capacity to observe natural phenomena has, therefore, played a crucial role in the development of science - the microscope being the paradigmatic example in biology. With the human genome, the natural world takes an unprecedented turn: it is better described as a sequence of symbols. Besides high-throughput machines such as sequencers and DNA chip readers, the computer and the associated software becomes the instrument to observe it, and the discipline of bioinformatics flourishes.”
Martin Reese and Roderic Guigó, Genome Biology 2006 7(Suppl I):S1,
introducing EGASP, the Encyclopedia of DNA Elements (ENCODE) Genome Annotation Assessment Project
We will study it in a variety of contexts including
Base pairs of DNA (billions)
>40b base pairs
Number of sequences
in GenBank (millions)
Base pairs of DNA in GenBank (billions)
Base pairs in GenBank + WGS (billions)
~200,000 species are represented in GenBank
Homo sapiens 13.1 billion bases
Bos taurus 5.2b
Zea mays 4.6b
Sus scrofa 3.6b
Oryza sativa (japonica)1.5b
Strongylocentrotus purpurata 1.4b
Nicotiana tabacum 1.1b
GenBank release 168.0
Excluding WGS, organelles, metagenomics
that integrates NCBI databases
Are made to Eukaryotic mRNAs?
-used to clone large pieces of DNA
Orthologous vs Paralogous Genes