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Molecular Biology

A beginner's intro to Bioinformatics
by

Amit Zur

on 7 February 2011

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Transcript of Molecular Biology

Computational Biology Connection between Biology and Computer Science DNA RNA Proteins Sugar Chromosomes Ribosome Mitochondria Cell Biological Substances Membrane Enzymes Biological Processes

DNA Replication

Transcription Translation Mutation Evolution Adaptation Diffusion Mitosis Meiosis Krebs Cytric Acid Cycle Glycolysis Mitochondrial Electron Transport Protein folding Algorithms Models Biological 4 Aspects Algorithmic Learning Statistics How to differentiate true phenomena from artifacts How to perform the task efficiently? How to adapt/estimate/learn parameters and models describing the task from examples? What is the task? Biological Sequence Comparison Algorithmic Learning Statistics When we compare to ~1 million sequences, what is a random match and what is true? Consider all ways to "align" one sequence against another How do we define "similar" sequences? Use examples to define similarity Evolution preserves sequences, thus similar genes might have similar function For example... History Recombination Kinase ligase Nuclease Helicase Topoisomerase Polymerage Virus 1857 "Genetics" by Mendel 1869 Identification of "Nuclein" 1882 Discovery of chromosomes 1919 "Nuclein" components are revealed - DNA!! 1943 DNA is the "genetic material" (?) 1953 DNA is a double-helix and very complex! 1957 The "Central Dogma of Biology" A C G T 1955 - DNA sequence of bovine(cow) Insulin 1958 - Protein sequence of Myoglobin 1960 - starting to predict protein structure

Atlas of sequences... 1970 - Protein Data Bank 1995 - first whole genome: Hemophilis Influenza
1996 - Yeast Genome 2001 - Human Genome Sickle Cell Anemia Comparative Genomics Sequence Alignment Algorithms What? Why? How? Practice the Algorithm Pairwise Alignment
Multiple Alignment
Scoring Matrix RefSeq
http://www.ncbi.nlm.nih.gov Genome Browser
http://www.genome.ucsc.edu/
Until 2009, more than 1700 biological databases are found in the web Database of biological databases!
http://www.biodbs.info/DS.html DNA, RNA & Protein sequences
Protein & RNA structure
Gene expression
Protein localization
Mutations
Similarity between species
Specie Specific database Entrez
http://www.ncbi.nlm.nih.gov/Entrez/
RefSeq
OMIM - genetic disorders
PDB - Protein Data Bank
GenBank - Genomic Data
PubMed - Literature
Uni-Prot - Protein Sequences
GEO - Gene Expression
Full transcript