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Visualizing Biosciences

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 :

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Visualizing Biosciences

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  1. Visualizing Biosciences Genomics & Proteomics

  2. “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?

  3. 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

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

  5. Entrez Genome Browser - National Center for Biotechnology Information,National Institutes of Health - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi • Ensembl Genome Browser -European Molecular Biology Laboratory - http://www.ensembl.org/ • TIGR Genome Maps – The Institute for Genetic Research - http://www.tigr.org/tdb/tgi/map.shtml • Human Protein Reference Database - http://www.hprd.org/

  6. NCBI Map Viewer http://www.ncbi.nlm.nih.gov/mapview/

  7. NCBI Map Viewer http://www.ncbi.nlm.nih.gov/mapview/

  8. NCBI Map Viewer http://www.ncbi.nlm.nih.gov/mapview/

  9. NCBI BLAST

  10. NCBI BLAST http://www.ncbi.nlm.nih.gov/BLAST/

  11. NCBI BLAST http://www.ncbi.nlm.nih.gov/BLAST/

  12. NCBI BLAST http://www.ncbi.nlm.nih.gov/BLAST/

  13. NCBI BLAST http://www.ncbi.nlm.nih.gov/BLAST/

  14. Commercial visualization tools: • metalife

  15. NCBI Map Viewer http://www.ncbi.nlm.nih.gov/mapview/

  16. metalife genome viewer http://metalife.orbitel.bg/

  17. metalife genome viewer http://metalife.orbitel.bg/

  18. metalife genome viewer http://metalife.orbitel.bg/

  19. metalife protein viewer http://metalife.orbitel.bg/

  20. metalife protein predictor – protein interaction sites http://metalife.orbitel.bg/

  21. protein interaction diagram http://www.hprd.org

  22. metalife interaction viewer http://metalife.orbitel.bg/

  23. metalife interaction viewer http://metalife.orbitel.bg/

  24. Commercial visualization tools: • metalife • DNAStar

  25. DNAStar BLAST http://www.dnastar.com

  26. DNAStar sequence alignment http://www.dnastar.com

  27. DNAStar GenVision 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 277:1453-1462, 1997.

  28. “Genetics Aesthetics” Visual maps of genomic information. e.g. Genomic Cartography by Benjamin Fry, Aesthetics & Computation Group, MIT Media Lab http://acg.media.mit.edu/people/fry/genocarto.html

  29. genomic cartography: axonometric introns and exons http://acg.media.mit.edu/people/fry/genocarto.html

  30. genomic cartography: handheld genome browser http://acg.media.mit.edu/people/fry/genocarto.html

  31. genomic cartography: genome valence http://acg.media.mit.edu/people/fry/genocarto.html

  32. The future is now?

  33. The future is now? http://acg.media.mit.edu/people/fry/genocarto.html

  34. The future is now? http://acg.media.mit.edu/people/fry/genocarto.html

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