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Computational Biology, Part 1Introduction
Computational Biology, Part 1Introduction
Robert F. MurphyRobert F. Murphy
Copyright Copyright 1996, 2000, 2001. 1996, 2000, 2001.
All rights reserved.All rights reserved.
Course IntroductionCourse Introduction
What these courses are aboutWhat these courses are about What I expectWhat I expect What you can expectWhat you can expect
What these courses are aboutWhat these courses are about
overview of ways in which computers are overview of ways in which computers are used to solve problems in biologyused to solve problems in biology
supervised learning of illustrative or supervised learning of illustrative or frequently-used programsfrequently-used programs
(03-510) supervised learning of (03-510) supervised learning of programming techniques and algorithms programming techniques and algorithms selected from these usesselected from these uses
I expectI expect
students will have basic knowledge of biology and chemistry students will have basic knowledge of biology and chemistry (at the level of Modern Biology/Chemistry) and willingness (at the level of Modern Biology/Chemistry) and willingness to learn moreto learn more
students will have basic familiarity with use of computers students will have basic familiarity with use of computers (e.g., at the level of Computing Skills Workshop) and (e.g., at the level of Computing Skills Workshop) and eagerness to gain new skillseagerness to gain new skills
(03-510) students have some programming experience and (03-510) students have some programming experience and willingness to work to improve willingness to work to improve
heterogeneous class - I plan to include refreshers on each heterogeneous class - I plan to include refreshers on each new topicnew topic
students will ask questions in class and via emailstudents will ask questions in class and via email
You can expectYou can expect Three major course sectionsThree major course sections
Sequence Analysis (13 classes)Sequence Analysis (13 classes) Biological Modeling (11 classes)Biological Modeling (11 classes) Biological Imaging (4 classes)Biological Imaging (4 classes)
Class sessions: lectures/demonstrations/exercises/quizzesClass sessions: lectures/demonstrations/exercises/quizzes Homework assignmentsHomework assignments
4 homework assignments for 03-311 (80% of grade)4 homework assignments for 03-311 (80% of grade) 8 homework assignments for 03-310 (70% of grade)8 homework assignments for 03-310 (70% of grade) 10 homework assignments for 03-510 (70% of grade)10 homework assignments for 03-510 (70% of grade)
Test Test March 1 March 1 (20% for 03-311, 10% for others)(20% for 03-311, 10% for others) Final (20% of grade for 03-310, 03-510)Final (20% of grade for 03-310, 03-510) Communication on class matters via email listCommunication on class matters via email list
Textbooks for first half of courseTextbooks for first half of course
For 03-310/311 studentsFor 03-310/311 students ““Required textbook” is Baxevanis & OuelletteRequired textbook” is Baxevanis & Ouellette
For 03-510 studentsFor 03-510 students ““Recommended” textbook is Durbin et al.Recommended” textbook is Durbin et al.
Additional suggested bookAdditional suggested book Computational Molecular Biology, Peter Clote & Computational Molecular Biology, Peter Clote &
Rolf Backofen (ISBN 0-471-87252-0)Rolf Backofen (ISBN 0-471-87252-0) Chap. 1 is an excellent introduction to Molec. Biol. for Chap. 1 is an excellent introduction to Molec. Biol. for
non-Biology majorsnon-Biology majors
Specific sources for CMU computational biology classesSpecific sources for CMU computational biology classes Web page Web page ((http://www.bio.cmu.edu/Courses/03310http://www.bio.cmu.edu/Courses/03310 or or
0331103311 or or 0351003510))
Lecture Notes (as PowerPoint files)Lecture Notes (as PowerPoint files) Homework Assignments (as Word files)Homework Assignments (as Word files) Additional materials as neededAdditional materials as needed
FTP server (FTP server (www.bio.cmu.eduwww.bio.cmu.edu)) Files needed for homework assignmentsFiles needed for homework assignments
CompBiol project volume on AFSCompBiol project volume on AFS /afs/andrew.cmu.edu/usr/murphy/CompBiol/afs/andrew.cmu.edu/usr/murphy/CompBiol
Additional classes for 03-510Additional classes for 03-510
We will have one additional class meeting We will have one additional class meeting per week for 03-510 for the first half of the per week for 03-510 for the first half of the semester onlysemester only
Purpose is to cover some more advanced Purpose is to cover some more advanced material and programming assignmentsmaterial and programming assignments
Other relevant coursesOther relevant courses
Second half mini-course “Second half mini-course “47-863: Topics in Operations Research: Computational Biology” will be taught by Dr. R. Ravi” will be taught by Dr. R. Ravi Tuesday-Thursday 1:30-2:50 starting 3/13Tuesday-Thursday 1:30-2:50 starting 3/13 Recommended for 03-510 studentsRecommended for 03-510 students
Fall 2001 course on advanced topics in Fall 2001 course on advanced topics in computational molecular biology will be taught computational molecular biology will be taught by Dr. Dannie Durandby Dr. Dannie Durand Prerequisite: 03-310/311/510Prerequisite: 03-310/311/510
Information flowInformation flow
A major task in computational molecular A major task in computational molecular biology is to “decipher” information biology is to “decipher” information contained in biological sequencescontained in biological sequences
Since the nucleotide sequence of a genome Since the nucleotide sequence of a genome contains all information necessary to contains all information necessary to produce a functional organism, we should in produce a functional organism, we should in theory be able to duplicate this decoding theory be able to duplicate this decoding using computersusing computers
Review of basic biochemistryReview of basic biochemistry
Central Dogma: DNA makes RNA makes Central Dogma: DNA makes RNA makes proteinprotein
Sequence determines structure determines Sequence determines structure determines functionfunction
StructureStructure
macromolecular structure divided intomacromolecular structure divided into primaryprimary structure (1D sequence)structure (1D sequence) secondarysecondary structure (local 2D & 3D) structure (local 2D & 3D) tertiarytertiary structure (global 3D)structure (global 3D)
DNA composed of four DNA composed of four nucleotidesnucleotides or "bases": or "bases": A,C,G,TA,C,G,T
RNA composed of four also: A,C,G,U (T RNA composed of four also: A,C,G,U (T transcribed as U)transcribed as U)
proteins are composed of proteins are composed of amino acidsamino acids
DNA properties - base compositionDNA properties - base composition
Some properties of long, naturally-occuring Some properties of long, naturally-occuring DNA molecules can be predicted accurately DNA molecules can be predicted accurately given only the given only the base compositionbase composition, usually , usually expressed as eitherexpressed as either %GC %GC (the percent of all base pairs that are (the percent of all base pairs that are
G:C), orG:C), or GCGC (the (the mole fraction mole fraction of all bases that are of all bases that are
either G or C)either G or C) %GC %GC = 100*= 100*GCGC
DNA properties - melting temperature and buoyant densityDNA properties - melting temperature and buoyant density Two such properties areTwo such properties are
TTmm, the , the melting temperaturemelting temperature, defined as the , defined as the
temperature at which half of the DNA is single-temperature at which half of the DNA is single-stranded and half is double-strandedstranded and half is double-stranded TTmm ( (ooC) = 69.3 + 41 C) = 69.3 + 41 GCGC (for 0.15 M NaCl) (for 0.15 M NaCl)
00, the , the buoyant densitybuoyant density, defined as the density , defined as the density
of a solution in which a DNA molecule will feel of a solution in which a DNA molecule will feel no net force when centrifuged (the density at no net force when centrifuged (the density at the point in a density gradient at which the the point in a density gradient at which the DNA stops moving, or “bands”)DNA stops moving, or “bands”) 00 (g cm (g cm-3-3) = 1.660 + 0.098) = 1.660 + 0.098 GCGC (for CsCl)(for CsCl)
DNA structure - restriction mapsDNA structure - restriction maps
Restriction enzymes Restriction enzymes cut DNA at specific cut DNA at specific sequences.sequences.
A A restriction map restriction map is a graphical is a graphical description of the order and lengths of description of the order and lengths of fragments that would be produced by the fragments that would be produced by the digestion of a DNA molecule with one or digestion of a DNA molecule with one or more restriction enzymesmore restriction enzymes
Restriction map of a circular plasmid with one enzymeRestriction map of a circular plasmid with one enzyme
AccII AccII
AccII
AccII
AccII
AccII
AccII
AccIIAccII
AccII
AccII
pGEM4
Restriction map of all enzymes that cut only onceRestriction map of all enzymes that cut only once
AcsI ApoI EcoRIEcl136II EcoICRISacI SstI Acc65I Asp718I AvaI BcoI
AflIII
AlwNI
AhdI AspEI Eam1105IEclHKIBpmI GsuI BglI AviII FspIBspCIPvuIXorII
Eco255IScaI
Asp700IXmnI
SspI
AatII
EcoNI
BsmFIDsaIAor51HIEco47III
SgrAINgoAIVNgoMINaeINheIBsp1407IBsrGISspBI
pGEM4
TranscriptionTranscription
transcription is accomplished by RNA polymerasetranscription is accomplished by RNA polymerase RNA polymerase binds to RNA polymerase binds to promoterspromoters promoters have distinct regions "-35" and "-10"promoters have distinct regions "-35" and "-10" efficiency of transcription controlled by binding efficiency of transcription controlled by binding
and progression ratesand progression rates transcription start and stop affected by tertiary transcription start and stop affected by tertiary
structurestructure regulatory sequences can be positive or negativeregulatory sequences can be positive or negative
RNA processingRNA processing
eukaryotic genes are interrupted byeukaryotic genes are interrupted by intronsintrons these are "spliced" out to yield mRNAthese are "spliced" out to yield mRNA splicing done by spliceosomesplicing done by spliceosome splicing sites are quite degenerate but not all splicing sites are quite degenerate but not all
are usedare used
TranslationTranslation
conversion from RNA to protein is by conversion from RNA to protein is by codoncodon: 3 bases = 1 amino acid: 3 bases = 1 amino acid
translation done by ribosometranslation done by ribosome translation efficiency controlled by mRNA translation efficiency controlled by mRNA
copy number (turnover) and ribosome copy number (turnover) and ribosome binding efficiencybinding efficiency
translation affected by mRNA tertiary translation affected by mRNA tertiary structurestructure
Protein localizationProtein localization
leader sequences can specify cellular leader sequences can specify cellular location (e.g., insert across membranes)location (e.g., insert across membranes)
leader sequences usually removed by leader sequences usually removed by proteolytic cleavageproteolytic cleavage
Postranslational processingPostranslational processing
peptides fold after translation - may be peptides fold after translation - may be assisted or unassistedassisted or unassisted
processing enzymes recognize specific sites processing enzymes recognize specific sites (amino acid sequences)(amino acid sequences)
protein signals can involve secondary and protein signals can involve secondary and tertiary structure, not just primary structuretertiary structure, not just primary structure
Goals of Sequence AnalysisGoals of Sequence Analysis
Assigned Reading:Assigned Reading: Baxevanis & Ouellette, Chapter 10Baxevanis & Ouellette, Chapter 10
Goals of Sequence AnalysisGoals of Sequence Analysis
Management of sequence informationManagement of sequence information Assembly of sequence fragments into complete Assembly of sequence fragments into complete
units (proteins, genes, chromosomes)units (proteins, genes, chromosomes)
Goals of Sequence AnalysisGoals of Sequence Analysis
Confirmation and prediction of restriction enzyme Confirmation and prediction of restriction enzyme sites (for nuc.acids)sites (for nuc.acids) can aid sequence determination in areas of uncertainty can aid sequence determination in areas of uncertainty
by permitting testing of specific basesby permitting testing of specific bases can permit selection of appropriate enzymes for can permit selection of appropriate enzymes for
sequence checkingsequence checking can permit selection of appropriate enzymes for can permit selection of appropriate enzymes for
subcloning or generation of probessubcloning or generation of probes
Goals of Sequence AnalysisGoals of Sequence Analysis
Finding open reading frames (ORFs) for cDNAs or Finding open reading frames (ORFs) for cDNAs or genomic DNA from organisms without intronsgenomic DNA from organisms without introns
Finding protein coding regions in DNAs using codon Finding protein coding regions in DNAs using codon usage tablesusage tables not all ORFs are made into proteinsnot all ORFs are made into proteins redundancy in genetic code is not fully reflected in the tRNAs redundancy in genetic code is not fully reflected in the tRNAs
made by a particular organism (codon preference)made by a particular organism (codon preference) can use to identify "real" coding regions (pseudo-genes "drift" in can use to identify "real" coding regions (pseudo-genes "drift" in
their codon usage)their codon usage) can use expressed sequence tags (ESTs)can use expressed sequence tags (ESTs)
Goals of Sequence AnalysisGoals of Sequence Analysis
Finding and using consensus sequencesFinding and using consensus sequences ExamplesExamples
promoterspromoters transcription initiation sitestranscription initiation sites transcription termination sitestranscription termination sites polyadenylation sitespolyadenylation sites ribosome binding sitesribosome binding sites protein featuresprotein features
use sets of sequences identified (by other means) as relateduse sets of sequences identified (by other means) as related use sets of sequences identified by sequence comparisonuse sets of sequences identified by sequence comparison
Goals of Sequence AnalysisGoals of Sequence Analysis
Comparison and alignment of sequencesComparison and alignment of sequences compare sequence to database - goal: find related compare sequence to database - goal: find related
sequences (SIMILARITY)sequences (SIMILARITY) compare sequence to sequence - goal: find matching compare sequence to sequence - goal: find matching
domains (ALIGNMENT)domains (ALIGNMENT) compare database to database - goal: estimate genetic compare database to database - goal: estimate genetic
distance (EVOLUTION)distance (EVOLUTION) either: determine consensus sequenceseither: determine consensus sequences comparisons can be pairwise or multiple-strandcomparisons can be pairwise or multiple-strand
Goals of Sequence AnalysisGoals of Sequence Analysis
Translation to protein sequence and prediction of Translation to protein sequence and prediction of protein properties - use measured propensities of protein properties - use measured propensities of particular amino acids or amino acid stretchesparticular amino acids or amino acid stretches Predict molecular weightPredict molecular weight Predict isoelectric point (pI)Predict isoelectric point (pI) Predict extinction coefficientPredict extinction coefficient
Prediction of secondary and tertiary structurePrediction of secondary and tertiary structure RNA - use base pairing energiesRNA - use base pairing energies protein - use propensitiesprotein - use propensities
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