Why bioinformatics ?

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New Insights in Bioinformatics Metsada
Pasmanik-Chor Bioinformatics Unit, Life Science,
TAU

• Topics
• Why bioinformatics ?
• Classical bioinformatics-
• similarity, conserved
• regions and alignments
• The post-genome era-
• high throughput tools and
• complex system analysis

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From Sequences to Functional Proteins - the
Central Dogma of Molecular Biology
CGCCAGCTGGACGGGCACACCATGAGGCTGCTGACCCTCCTGGGCCTTCT
GTGTGGCTCGGTGGCCACCCCCTTAGGCCCGAAGTGGCCTGAACCTGTGT
TCGGGCGCCTGGCATCCCCCGGCTTTCCAGGGGAGTATGCCAATGACCAG
GAGCGGCGCTGGACCCTGACTGCACCCCCCGGCTACCGCCTGCGCCTCTA
CTTCACCCACTTCGACCTGGAGCTCTCCCACCTCTGCGAGTACGACTTCG
TCAAG
Sequence data Strings of letters
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The Biotechnology Revolution Requires
Bioinformatics Advancement
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The Human Genome Project (HGP)

• Goals
• Sequence the human genome
• Identify all genes
• Predict gene function
• Determine involvement
• in human diseases.
• Note
• Only 1 fully achieved so far

Francis Collins (head of public project, NIH)
I think this is probably the most important
scientific effort that mankind has ever mounted.
That includes splitting the atom and going to the
moon.
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The Human Genome Project ELSI
Address the Ethical, Legal, and Social
Implications (ELSI) that may arise from the HGP.
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DNA Variability SNPs and the HapMap Project

• DNA is identical in all cells of an
• individual, and almost identical among
• different individuals of same species
• (99.9 in humans).

• For a variation to be considered
• SNP, it must occur in at least 1
• of the population.

The HapMap is a catalog of common genetic
variants (haplotypes) in human, and their
associations. Goal Understand polymorphisms
in terms of potential functionality, and
relevance to human health.
http//www.nature.com/nature/journal/v437/n7063/pd
f/4371241a.pdf
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DNA Variability SNPs and the HapMap Project
Example of visualization for a non-synonymous SNP
from alcohol dehydrogenase (PDB code 1htb).
Surface pocket
R mutation47
Nucleic Acids Res. 2004 January 1 32 (Database
issue) D520D522 http//www.pubmedcentral.nih.gov
/articlerender.fcgi?artid308838
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Sequenced Genomes
No. of genes



How Many Sequenced Genomes? Currently (May
20th, 2007) 558 complete genomes
available and more than 2,500 on-going
projects !
Eukarya Bacteria Archea
49 468 41
http//www.genomesonline.org/
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Mouse and Human Not So Far Apart
Approx. 150 cut and paste operations will
transform humans into mice.
http//www.public.iastate.edu/semrich/compgen/cg
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