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Biol 465 - Notes for the course

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BIOL 465
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Index of content21IntroductionBioinformatics applicationssequence alignmentssequence comparisonsclustering and phylogenetic treesgene finding evolutionary histories functional annotationpattern analysisRandom examples LC MS Digest liquid chromatography Ensemblecomparative genomicsmapping blockswhere are chromosome areas found in other organisms Mouse model organisms Protein structure modelingGenotype analysisGene regulation analysisSystems biology Homology recognitiongloballocal sequence Alignments Needleman wunschsmith watermanBlastheuristic homology search Several variancesWU blast is good for over 65identityBased on two models Homology or notSubstitution matrices PP or NN PAM and BLOSUM PAM HIGH QUALITY SINGEL CHANGE EXTRAPOLATION BLOSUM for Database searchB62 best compromiseUse of log odd values is more easy than using no log values additionHomology modeling of proteinsModel the protein structure based on known structure of known proteinsWhen sequence homology is found you know they are related Homology is a es and no question Log odd is zero if a occurrence is the same as random matching Training setwhat is that Test set of data Gap penalties are heuristic as well 2Dynamic programmingWe have a DNA or protein sequence and we want to calculate a score that reflects how similar they are Thus how likely it is that they are derived from a common ancestor Because there are 3
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