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Introduction to Bioinformatics

by: Gerda Bernier

Introduction to Bioinformatics COMP SCI 576

Gerda Bernier
GPA 3.98

Colin Dewey

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Colin Dewey
Class Notes
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This 33 page Class Notes was uploaded by Gerda Bernier on Thursday September 17, 2015. The Class Notes belongs to COMP SCI 576 at University of Wisconsin - Madison taught by Colin Dewey in Fall. Since its upload, it has received 46 views. For similar materials see /class/205105/comp-sci-576-university-of-wisconsin-madison in ComputerScienence at University of Wisconsin - Madison.

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Date Created: 09/17/15
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ag i quotg 39 ui Erogden Paycholusy L k A RandallA W D I39un L Expec red Background CS 367 In rro ro Da ra S rruc rures or equivalen r s ra ris rics good if you39ve had a r leas r one course bu r not required molecular biology no knowledge assumed but an in reres r in learning some basic molecular biology is manda rory Course Emphases understanding the rypes and sources of da ra available For compula rional biology unders randing rhe impor ran r compula rional problems in molecular biology unders randing rhe mos r signi can r amp in reres ring algori rhms Course Requiremen rs 6 homework assignmen rs 50 mos rly programming some wri r ren exercises mid rerm exam 20 nal exam 30 Par ricipa rion A r rending lectures is Lo op rional A signi can r amoun r of ma rerial is not in the slides eg board work Please par ricipa re during class Compu ring Resources For rhe Class UNIX works ra rions in Dept of Bios ra ris rics amp Medical Informatics no lab mus r log in remo rely wi rh SSH accoun rs will be crea red la rer this week rwo servers you can log in ro mi1bios ra rwiscedu mi2bios ra rwiscedu UNIX Help CS depar rmen r usually offers UNIX orien ra rion sessions during rs r rwo weeks of classes CS 1000 UNIX ru rorial h r rpwwwcswisceducslcsIOOO Programming Languages For programming exercises you mus r use one of C C Java Perl Python These are The s randard bioinForma rics languages Course Readings Biological 39 Biological Sequence Analysis sequence Probabilistic Models of Pro reins and Nucleic Acids R Durbin S Eddy A Krogh and G Mi rchison Cambridge Universi ry Press 1998 ar ricles From The primary li rera rure scien ri c journals e rc G Mitchison Exams Mid rerm Friday Oc rober 30th In class Final Sa rurday December 19th 745945am NO MAKEUP EXAMS Who r is BioinFormo rics represen ro rions roragere rrievalanalysis of biological do ro concerning sequences slruclures Func rions ac rivi ry levels ne rworks of in remc rions oFamong biomolecules some rimes used synonymoust wi rh compu ro rional biology or compu ro rional molecular biology BioinForma rics Topics Topic Lecires Molecules Genome Assembly 4 DNA Sequence Alignmen r 7 DNAPro rein Sequence Anno ra rion 8 DNA Phylogene ric Trees 6 DNAPro rein Gene Expression 5 RNA Cellular Ne rworks 6 RNAPro rein Pro rein S rruc rure 3 Pro rein Compu rer Science Topics Algori rhms Graphs Exacf Greedy Dynamic Programming Branch and bound Heuris rics Compu ra rional Complexi ry S ra ris rics Topics Probabili ry For discre re random variables Markov Chains Hidden Markov Models Maximum Likelihood Expec ra rionMaximiza rion Bayesian ne rworks Sequence Assembly How do we defermine fhe genome sequence 0F an organism Wha r do rwo sequences genomes have in common Sequence Alignmen r Topics pairwise and mulliple sequence alignmen r dynamic programming me rhods For global and local alignmen rs linear and af ne gap penal ry Func rions lhe BLAST algori rhm dynamic programming and heuris ric me rhods For mulliple sequence alignmen r alignmen r s ra ris rics and subs ri ru rion ma rrices Where are rhe genes in rhis genome Echrv Base Position l Chromosome Band 8T3 Markers spliced ESTS Conservation chimp dog I mouse I ll rat chicken USU 7nhra iqh 127475886 1274Baeeel 127485989 x274eeeeel on Pomosome Bands Localized DH FISH 7 321 STS Markers on Genetic blue and Radiation Hngid black Fps Gap Locations LEP Fefseq Genes r Gensca1 Gene Predictions l I l l A I l I I I l I Human nRN s From GenBank U43653 80868839 80969323 80969452 8096952 F888123 D4948 LI 1 89 1 5 Human E8 5 That Have Been spliced HuChimpimouseRatIDogIChickfFuguiZFish Multiz lignments amp Conservation 1274gseae Known Genes Based on SEISS PROT TPEMBL mRN and ReFSeq 127seeeaal 127585698 Mapping Clones H H I Probabilis ric Sequence Model Topics Markov chains highorder Markov models inhomogeneous Markov models hidden Markov models ForwardBackwardVi rerbi algori rhms applica rions ro gene nding and mo riF modeling m mm man Mam How are fhese sPeCies relafed New Wand la e 7mm mum Kmmw uwisubuuummrsvm Phylogene ric Tree InFerence Topics dis rancebased approaches parsimonybased approaches branchandbound search mul riple sequence alignmen r Can diseases be characterized a by pa r rerns oF gene ac rivi ry Topics in Data Analysis From HighThroughput Experiments clustering algorithms hierarchical clustering kmeans clustering EM based clustering classi cation algorithms simple methods For supervised learning multiple hypothesis testing and the False discovery rate Can we infer models oF cellular processes From highH39n ougl39lpunL experimenls cell model r 313w r n H i PI3Klt gt RAS Cytohesip JAB1 33 L Zap70 VAV Lek SLP76 N ll L MAPKKK A Inhibitors l a 6 606976 7 AKT inh MEK47 8 Psitect l 39 l 9 U0126 10 LY294002 Ne rwork Modeling Topics Bayesian ne rwork represenfa rions algorithms For exac r inference in BNs algori rhms For s rruc rure and parame rer learning in BNs Wha r does The pro rein encoded by a given gene look like Wha r does i r do Protein Structure Prediction Topics classi cation methods revisited threading algorithms the Rosetta system The Shor r rerm Plan Friday 94 and Wednesday 99 Molecular Biology 101quot lec rures Op rional For biology s ruden rs Friday 911 s rar r on Sequence Assemblyquot Assignmen rs Reading Life and I rs Molecules A Brie1c In rroduc rion L Hun rer Available From web page Homework Homework 0 Due nex r Wednesday To make sure you know how To use your course accoun r


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