Visualizing Biosciences Genomics & Proteomics. “Scientists Complete Rough Draft of Human Genome” - New York Times, June 26, 2000 The problem: –3 billion.

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Presentation transcript:

Visualizing Biosciences Genomics & Proteomics

“Scientists Complete Rough Draft of Human Genome” - New York Times, June 26, 2000 The problem: –3 billion base pairs (ACGT) –~40,000 genes (?) –How do we decipher them? –What do they mean? –How can the information be used?

genomics : The study of all of the nucleotide sequences, including structural genes, regulatory sequences, and noncoding DNA segments, in the chromosomes of an organism. proteomics: Description and functional characterization of the full complement of an organism’s proteins

Some types of BioViz Publicly available visualization tools Commercial visualization tools “Genetics Aesthetics”

Entrez Genome Browser - National Center for Biotechnology Information,National Institutes of Health - Ensembl Genome Browser - European Molecular Biology Laboratory - TIGR Genome Maps – The Institute for Genetic Research - Human Protein Reference Database -

NCBI Map Viewer

NCBI Map Viewer

NCBI Map Viewer

NCBI BLAST

NCBI BLAST

NCBI BLAST

NCBI BLAST

NCBI BLAST

Commercial visualization tools: metalife

NCBI Map Viewer

metalife genome viewer

metalife genome viewer

metalife genome viewer

metalife protein viewer

metalife protein predictor – protein interaction sites

protein interaction diagram

metalife interaction viewer

metalife interaction viewer

Commercial visualization tools: metalife DNAStar

DNAStar BLAST

DNAStar sequence alignment

Figure 1. The overall structure of the E. coli genome. The origin and terminus of replication are shown as green lines, with blue arrows indicating replichores 1 and 2. A scale indicates the coordinates both in base pairs and in minutes (actually centisomes, or 100 equal intervals of the DNA). The distribution of genes is depicted on two outer rings: The orange boxes are genes located on the presented strand, and the yellow boxes are genes on the opposite strand. Red arrows show the location and direction of transcription of rRNA genes, and tRNA genes are shown as green arrows. The next circle illustrates the positions of REP sequences around the genome as radial tick marks. The central orange sunburst is a histogram of inverse CAI (1 - CAI), in which long yellow rays represent clusters of low (<0.25) CAI. The CAI plot is enclosed by a ring indicating similarities between previously described bacteriophage proteins and the proteins encoded by the complete E. coli genome; the similarity is plotted as described in Fig. 3 for the complete genome comparisons. The complete genome sequence of Escherichia coli K-12. Blattner et al., Science 277: , DNAStar GenVision

“Genetics Aesthetics” Visual maps of genomic information. e.g. Genomic Cartography by Benjamin Fry, Aesthetics & Computation Group, MIT Media Lab

genomic cartography: axonometric introns and exons

genomic cartography: handheld genome browser

genomic cartography: genome valence

The future is now?

The future is now?

The future is now?