生物信息学课程ScoringAlignmentBioinformaticsGAATCGAAT-C-GAAT-CCATACC-ATACC-A-TACGAATC-GAAT-CGA-ATCCA-TACCA-TACCATA-CScoring function: measure the quality of a given alignment? Scoring matrix,.Gap penalty16
16 生物信息学 课程 Bioinformatics Scoring Alignment Scoring function: measure the quality of a given alignment. • Scoring matrix, • Gap penalty GAATC GAAT-C -GAAT-C CATAC C-ATAC C-A-TAC GAATC- GAAT-C GA-ATC CA-TAC CA-TAC CATA-C
生物信息学课程Scoring MatrixBioinformatics·Scoring a substitution.Measure the likelihood of a given substitution happened intherealworld·Substitutions that are more likely should get a higher score·Substitutions that are lesslikely should get a lower scoreScoringMatricesaredesignedtodetectsignal abovebackground, i.e. to detect similarities beyond what would beobservedbychancealone17
17 生物信息学 课程 Bioinformatics Scoring Matrix • Scoring a substitution • Measure the likelihood of a given substitution happened in the real world. • Substitutions that are more likely should get a higher score • Substitutions that are less likely should get a lower score • Scoring Matrices are designed to detect signal above background, i.e. to detect similarities beyond what would be observed by chance alone
生物信息学课程NucleotideScoring MatrixBioinformaticsTransversionPurineAGPyrimidineAhypotheticalsubstitutionmatrix:cGTATransition2-7-5-7A2c-7-7-5GAATC-5-72-7GCATCC-7-5-72T-7 + 2 + (-7) + (-5) + 2 = -1518
生物信息学 课程 Bioinformatics Purine A G Pyrimidine C T Transversion A C G T A 2 -7 -5 -7 C -7 2 -7 -5 G -5 -7 2 -7 T -7 -5 -7 2 A hypothetical substitutionmatrix: Transition GAATC CATCC -7 + 2 + (-7) + (-5) + 2 = -15 Nucleotide Scoring Matrix 18
生物信息学课程Amino acid Scoring matrixBioinformaticsAminoAcidsAalanine (ala)HydroxylicRarginine (arg)TinyNasparagine (asn)PDasparticacid(asp)SmallC cysteine (cys)AliphaticGAQglutamine(gln)Eglutamic acid (glu)SAcidicGglycine (gly)CHhistidine (his)NTisoleucine (ile)SulphurDQLleucine (leu)ContainingK lysine (lys)MEMmetioneine(met)YKHAromaticRFphenyalanine(phe)FWPositivePproline(pro)S serine (ser)(Basic)HydrophobicTthreonine (thr)PolatWtrytophan(trp)ChargedYtyrosine (tyr)(AdoptedfromProf.JingchuLuo)19
生物信息学 课程 Bioinformatics Amino acid Scoring matrix (Adopted from Prof. JingchuLuo) 19
生物信息学课程PAM:ScoringbyevolutionaryBioinformaticsdistance·PAM:PercentAcceptedMutation.Two sequences are 1 PAM apart if they differ in 1 % of theresidues..1PAM=onestepofevolution1%mismatch20
生物信息学 课程 Bioinformatics PAM: Scoring by evolutionary distance • PAM: Percent Accepted Mutation • Two sequences are 1 PAM apart if they differ in 1 % of the residues. • 1 PAM = one step of evolution 1% mismatch 20