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Computational Biology, Part 1 Introduction Robert F. Murphy Copyright 1996, 2000, 2001. All rights reserved. Course Introduction What these courses are about What I expect What you can expect What these courses are about overview of ways in which computers are used to solve problems in biology supervised learning of illustrative or frequently-used programs (03-510) supervised learning of programming techniques and algorithms selected from these uses I expect students will have basic knowledge of biology and chemistry (at the level of Modern Biology/Chemistry) and willingness to learn more students will have basic familiarity with use of computers (e.g., at the level of Computing Skills Workshop) and eagerness to gain new skills (03-510) students have some programming experience and willingness to work to improve heterogeneous class - I plan to include refreshers on each new topic students will ask questions in class and via email You can expect Three major course sections Class sessions: lectures/demonstrations/exercises/quizzes Homework assignments Sequence Analysis (13 classes) Biological Modeling (11 classes) Biological Imaging (4 classes) 4 homework assignments for 03-311 (80% of grade) 8 homework assignments for 03-310 (70% of grade) 10 homework assignments for 03-510 (70% of grade) Test March 1 (20% for 03-311, 10% for others) Final (20% of grade for 03-310, 03-510) Communication on class matters via email list Textbooks for first half of course For 03-310/311 students “Required textbook” is Baxevanis & Ouellette For 03-510 students “Recommended” textbook is Durbin et al. Additional suggested book Computational Molecular Biology, Peter Clote & Rolf Backofen (ISBN 0-471-87252-0) Chap. 1 is an excellent introduction to Molec. Biol. for non-Biology majors Specific sources for CMU computational biology classes Web page (http://www.bio.cmu.edu/Courses/03310 or 03311 or 03510) Lecture Notes (as PowerPoint files) Homework Assignments (as Word files) Additional materials as needed FTP server (www.bio.cmu.edu) Files needed for homework assignments CompBiol project volume on AFS /afs/andrew.cmu.edu/usr/murphy/CompBiol Additional classes for 03-510 We will have one additional class meeting per week for 03-510 for the first half of the semester only Purpose is to cover some more advanced material and programming assignments Other relevant courses Second half mini-course “47-863: Topics in Operations Research: Computational Biology” will be taught by Dr. R. Ravi Tuesday-Thursday 1:30-2:50 starting 3/13 Recommended for 03-510 students Fall 2001 course on advanced topics in computational molecular biology will be taught by Dr. Dannie Durand Prerequisite: 03-310/311/510 Information flow A major task in computational molecular biology is to “decipher” information contained in biological sequences Since the nucleotide sequence of a genome contains all information necessary to produce a functional organism, we should in theory be able to duplicate this decoding using computers Review of basic biochemistry Central Dogma: DNA makes RNA makes protein Sequence determines structure determines function Structure macromolecular structure divided into primary structure (1D sequence) secondary structure (local 2D & 3D) tertiary structure (global 3D) DNA composed of four nucleotides or "bases": A,C,G,T RNA composed of four also: A,C,G,U (T transcribed as U) proteins are composed of amino acids DNA properties - base composition Some properties of long, naturally-occuring DNA molecules can be predicted accurately given only the base composition, usually expressed as either %GC (the percent of all base pairs that are G:C), or GC (the mole fraction of all bases that are either G or C) %GC = 100*GC DNA properties - melting temperature and buoyant density Two such properties are Tm, the melting temperature, defined as the temperature at which half of the DNA is singlestranded and half is double-stranded Tm (oC) = 69.3 + 41 GC (for 0.15 M NaCl) 0, the buoyant density, defined as the density of a solution in which a DNA molecule will feel no net force when centrifuged (the density at the point in a density gradient at which the DNA stops moving, or “bands”) 0 (g cm-3) = 1.660 + 0.098 GC (for CsCl) DNA structure - restriction maps Restriction enzymes cut DNA at specific sequences. A restriction map is a graphical description of the order and lengths of fragments that would be produced by the digestion of a DNA molecule with one or more restriction enzymes Restriction map of a circular plasmid with one enzyme AccII AccII AccII AccII AccII AccII pGEM4 AccII AccII AccII AccII AccII Restriction map of all enzymes that cut only once SspBIBsrGI Bsp1407I AcsI ApoI EcoRI Ecl136II EcoICRISacI SstI Acc65I Asp718I AvaI NheINaeINgoMINgoAIV SgrAI Eco47IIIAor51HI DsaI BsmFI EcoNI AflIII pGEM4 AlwNI AatII SspI XmnIAsp700I ScaI Eco255I XorII PvuI BspCI AhdI AspEI Eam1105I EclHKI BpmI GsuI BglI AviII FspI Transcription transcription is accomplished by RNA polymerase RNA polymerase binds to promoters promoters have distinct regions "-35" and "-10" efficiency of transcription controlled by binding and progression rates transcription start and stop affected by tertiary structure regulatory sequences can be positive or negative RNA processing eukaryotic genes are interrupted by introns these are "spliced" out to yield mRNA splicing done by spliceosome splicing sites are quite degenerate but not all are used Translation conversion from RNA to protein is by codon: 3 bases = 1 amino acid translation done by ribosome translation efficiency controlled by mRNA copy number (turnover) and ribosome binding efficiency translation affected by mRNA tertiary structure Protein localization leader sequences can specify cellular location (e.g., insert across membranes) leader sequences usually removed by proteolytic cleavage Postranslational processing peptides fold after translation - may be assisted or unassisted processing enzymes recognize specific sites (amino acid sequences) protein signals can involve secondary and tertiary structure, not just primary structure Goals of Sequence Analysis Assigned Reading: Baxevanis & Ouellette, Chapter 10 Goals of Sequence Analysis Management of sequence information Assembly of sequence fragments into complete units (proteins, genes, chromosomes) Goals of Sequence Analysis Confirmation and prediction of restriction enzyme sites (for nuc.acids) can aid sequence determination in areas of uncertainty by permitting testing of specific bases can permit selection of appropriate enzymes for sequence checking can permit selection of appropriate enzymes for subcloning or generation of probes Goals of Sequence Analysis Finding open reading frames (ORFs) for cDNAs or genomic DNA from organisms without introns Finding protein coding regions in DNAs using codon usage tables not all ORFs are made into proteins redundancy in genetic code is not fully reflected in the tRNAs made by a particular organism (codon preference) can use to identify "real" coding regions (pseudo-genes "drift" in their codon usage) can use expressed sequence tags (ESTs) Goals of Sequence Analysis Finding and using consensus sequences Examples promoters transcription initiation sites transcription termination sites polyadenylation sites ribosome binding sites protein features use sets of sequences identified (by other means) as related use sets of sequences identified by sequence comparison Goals of Sequence Analysis Comparison and alignment of sequences compare sequence to database - goal: find related sequences (SIMILARITY) compare sequence to sequence - goal: find matching domains (ALIGNMENT) compare database to database - goal: estimate genetic distance (EVOLUTION) either: determine consensus sequences comparisons can be pairwise or multiple-strand Goals of Sequence Analysis Translation to protein sequence and prediction of protein properties - use measured propensities of particular amino acids or amino acid stretches Predict molecular weight Predict isoelectric point (pI) Predict extinction coefficient Prediction of secondary and tertiary structure RNA - use base pairing energies protein - use propensities