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Protein Synthesis and Gene Finding Day 2

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  • ProteinSynthesisandGeneFinding

    Day2

  • DNAAnalysis

    •  23andMe•  Personalizedmedicine•  Geneticscreensfordisease•  Etc.

  • BioCrashCourse:DNA

    Photo51:X-raydiffractioncreatedbyRaymondGoslingunderthesupervisionofRosalindFranklinMay,1952

    DoubleHelixStructure:WatsonandCrick

  • DNAandtheCentralDogma

    TheblueprintsformakingalltheproteinsnecessaryforlifearecontainedwithinDNA.Or,moresuccinctly:DNAMakesRNA,RNAmakesProtein

  • ProteinsProteinsarechainsofAminoAcids

  • Aside:ProteinSecondaryStructurePrediction

    Fold-it:agameifiedapproachtocomputingthisstructure

    Goal:findthelowestenergyconfigurationofanaminoacidchain

    Unfortunatelythisproblemishard!Howhardisit?Thishard:http://www.cs.berkeley.edu/~christos/hp.ps

    https://www.youtube.com/watch?v=lGYJyur4FUA

  • ProteinogenicAminoAcids

    http://en.wikipedia.org/wiki/Amino_acid

  • DNAandProteinSynthesis

    •  Stage1:anenzyme“decides”thatitistimetosynthesizeaprotein(epigenetics)

    •  Stage2:DNAisunzippedandpairedwithacomplementarystrandofRNA(transcription)

    •  Stage3:tRNAattachesaminoacidstocomplementarysegmentsofRNA(translation)

  • ProteinSynthesisDetailedExample

    5’ – AGCAATGTTCCAGATGTAATT – 3’

    3’ – TCGTTACAAGGTCTACATTAA – 5’

    Aside:The5’and3’areusefulwhentalkingaboutthedirectionalityofcertainprocessesrelatedtoproteinsynthesis.Morelater.

  • ProteinSynthesisStep1:TranscriptionInitiation

    5’ – AGCAATGTTCCAGATGTAATT – 3’

    3’ – TCGTTACAAGGTCTACATTAA – 5’

    ATGisalsoknownasthestartcodon.Thisiswheretranscriptionstarts.

    TemplateStrand

    SenseStrand

  • ProteinSynthesisStep2:MessengerRNAAttaches

    5’ – AGCA

    3’ – TCGTTACAAGGACTACATTAA – 5’

    ATGTTCCT

    GATGTAAT

    T – 3’

    AUGUUCCUGAUGUAAUU – 3’

    ThisnewstrandisknownasmessengerRNA

  • ProteinSynthesisStep3:MessengerRNABreaksAway

    5’ - AUGUUCCUGAUGUAAUU – 3’

  • ProteinSynthesisStep4:AminoAcidChainForms

    5’ - AUGUUCCUGAUGUAAUU – 3’

    UAC

    M

    AAG

    F

    GAC

    D

    UAC

    M

    StopCodonKnownasanOpenReadingFrame(ORF)

  • ProteinSynthesisSomethingstoNotice

    5’ - AUGUUCCUGAUGUAAUU – 3’

    UAC

    M

    AAG

    F

    GAC

    D

    UAC

    M

    StopCodonAnotherStartCodon(NestedReadingFrame)

    OutofframeStopcodon

  • DNACodonTable

    Thiscodeisreadfrom5’to3’ontheDNAstrand

  • 6ReadingFrames:ReadingFrame1

    5’ – AGCAATGTTCCAGATGTAATT – 3’

    3’ – TCGTTACAAGGTCTACATTAA – 5’

    Codonsreadinthisdirection

  • 6ReadingFrames:ReadingFrame2

    5’ – AGCAATGTTCCAGATGTAATT – 3’

    3’ – TCGTTACAAGGTCTACATTAA – 5’

    Codonsreadinthisdirection

  • 6ReadingFrames:ReadingFrame3

    5’ – AGCAATGTTCCAGATGTAATT – 3’

    3’ – TCGTTACAAGGTCTACATTAA – 5’

    Codonsreadinthisdirection

  • 6ReadingFrames:ReadingFrame4

    5’ – AGCAATGTTCCAGATGTAATT – 3’

    3’ – TCGTTACAAGGTCTACATTAA – 5’

    Codonsreadinthisdirection

  • 6ReadingFrames:ReadingFrame5

    5’ – AGCAATGTTCCAGATGTAATT – 3’

    3’ – TCGTTACAAGGTCTACATTAA – 5’

    Codonsreadinthisdirection

  • 6ReadingFrames:ReadingFrame6

    5’ – AGCAATGTTCCAGATGTAATT – 3’

    3’ – TCGTTACAAGGTCTACATTAA – 5’

    Codonsreadinthisdirection

  • Mini-Project:GeneFinder!

    •  Createapythonprogramthatperformsabinitiogenefindingby– DeterminingwhichDNAsegmentslikelycodeforproteins

    – OutputtingtheaminoacidsequencescodedbytheseregionsofDNA

    •  Runtheseaminoacidsequencesthroughasearchenginetodeterminetheirfunction!

  • Ab-InitioGeneFindingStrategy

    •  Tell-talemarker:suspiciouslylongORFs•  Suspiciousisdefinedasbeingimprobabletofindinnon-codingDNA

  • (partof)Nexttime

    JoannePrattwillguestlectureonageneticsearchenginecalledBLAST(anditsuses)aswellastheroleofBLASTinstudyingpathogenesis.


Computational gene finding - Rice University

Ab initio gene prediction

Gene Finding in Eukaryotesubio.bioinfo.cnio.es/Cursos/cursoVerano2008/madrid08/gene_finding... · Gene Finding in Eukaryotes Jan-Jaap Wesselink [email protected] Computational and

Prokaryotic gene finding

Gene finding and gene structure prediction

Markov Models for Gene Finding...Interpolated Markov Models for Gene Finding Key concepts •the gene-finding task •the trade-off between potential predictive value and parameter

CSE 549: Models for ab initio Gene Finding · The Genetic Code • There are 20 different amino acids & 64 different codons. • Lots of different ways to encode for each amino acid

Gene Structure & Gene Finding: Part I

Ab initio gene prediction Genome 559, Winter 2011

Biological Motivation Gene Finding

Ab initio Gene Finding print - GEP Community Server

Outline Introduction to ab initio and evidence-based gene findingcommunity.gep.wustl.edu/.../Ab_initio_Gene_Finding.pdf · 2020. 1. 5. · Bootstrap with ab initio gene predictions

Finding “the gene” for cystic fibrosis

Eukaryotic Gene Finding Adapted in part from

Computational Gene Finding

CL662 PW 02 Gene Finding

Gene Finding and Sequence Annotation

Gene Finding

Finding the Happy Gene - Saligent Presentation

The Merck Gene Index browser: an extensible data integration system for gene finding, gene

Eukaryotic Gene Finding

Gene Structure Prediction (Gene Finding) I519 Introduction to Bioinformatics, 2012

Finding Regulatory Motifs in DNA Sequences. Motifs and Transcriptional Start Sites gene ATCCCG gene TTCCGG gene ATCCCG gene ATGCCG gene ATGCCC

Gene Structure & Gene Finding · Gene Structure & Gene Finding David Wishart Rm. 3-41 Athabasca Hall [email protected] Outline for Next 3 Weeks • Genes and Gene Finding

Ab initio vertebrate gene predictions the problem of big genes · Page 1 1 Ab initio vertebrate gene predictions — the problem of big genes Jun Wang,1,2,* ShengTing Li,1,* Yong

Bacterial Gene Finding and Glimmer (also Archaeal and viral gene finding)

Comparative Gene Finding

Computational Gene-Finding for Noncoding RNAs

Ab initio gene prediction - Borenstein Lab · 2011. 3. 3. · Ab initio gene prediction method •Define parameters of real genes (based on experimental evidence): •Use those parameters

Gnomon NCBI eukaryotic gene prediction tool · 1 Methods NCBI gene prediction is a combination of homology searching with ab initio modeling. The use of ab initio is threefold: a)

Gene Finding Genome Annotation. Gene finding is a cornerstone of genomic analysis Genome content and organization Differential expression analysis Epigenomics

Gene Structure Prediction (Gene Finding)

Biological Motivation Gene Finding in Eukaryotic Genomes

Disease Gene Finding. Table of contents:

Gene Finding Project (Cont.)