Practical Bioinformatics -...

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Hidden Markov Modelshisto.ucsf.edu/BMS270/BMS270a_2012/slides/Slides05_HMM.pdf · Hidden Markov Models Mark Voorhies 4/2/2012 Mark Voorhies Hidden Markov Models. Searching with PSI-BLAST

Hidden Markov Modelshisto.ucsf.edu/BMS270/BMS270a_2012/slides/Slides05_HMM.pdf · Hidden Markov Models Mark Voorhies 4/2/2012 Mark Voorhies Hidden Markov Models. Searching with PSI-BLAST

Scoring matrices Identity PAM BLOSUM. Scoring Matrices Types Identity matrix – exact matches receive one score and non-exat matches a different score.

Scoring matrices Identity PAM BLOSUM. Scoring Matrices Types Identity matrix – exact matches receive one score and non-exat matches a different score.

pam blosum 01 - unimi.ithomes.di.unimi.it/trucco/Bioinformatics/pam_blosum.pdf · Derivation)of)the)PAM)matrices Relative(amino(acid(mutability(values(mj forourexample Amino)acid

pam blosum 01 - unimi.ithomes.di.unimi.it/trucco/Bioinformatics/pam_blosum.pdf · Derivation)of)the)PAM)matrices Relative(amino(acid(mutability(values(mj forourexample Amino)acid

PAM & Blosum

PAM & Blosum

Scoring the Alignment of Amino Acid Sequences Constructing PAM and Blosum Matrices.

Scoring the Alignment of Amino Acid Sequences Constructing PAM and Blosum Matrices.

Why? Sequence Alignment - School of Informatics · Sequence Alignment Armstrong, 2008 Why? • Genome sequencing gives us new gene sequences ... – PAM and BLOSUM Armstrong, 2008

Why? Sequence Alignment - School of Informatics · Sequence Alignment Armstrong, 2008 Why? • Genome sequencing gives us new gene sequences ... – PAM and BLOSUM Armstrong, 2008

348-F - sanjesh.org · 348F AUG CAP UAG a. ATG ATTGG (pairwise alignment) , Jots PAM 10 PAM250(Ÿ BLOSUM 62 BLOSUM 10 Gap penalty —.S k (alignment) (Gap) - Bit score (Y

348-F - sanjesh.org · 348F AUG CAP UAG a. ATG ATTGG (pairwise alignment) , Jots PAM 10 PAM250(Ÿ BLOSUM 62 BLOSUM 10 Gap penalty —.S k (alignment) (Gap) - Bit score (Y

Bioinformatics 1: lecture 5 - Purdue University · Differences between PAM and BLOSUM PAM •PAM matrices are based on global alignments of closely related proteins. •The PAM1 is

Bioinformatics 1: lecture 5 - Purdue University · Differences between PAM and BLOSUM PAM •PAM matrices are based on global alignments of closely related proteins. •The PAM1 is

Single alignment: Substitution Matrix - UnivAQ · BLOSUM vs PAM PAM-BLOSUM differences: • An increasing index indicates PAM scores to more distant proteins among them (expressing

Single alignment: Substitution Matrix - UnivAQ · BLOSUM vs PAM PAM-BLOSUM differences: • An increasing index indicates PAM scores to more distant proteins among them (expressing

Scoring Matrices June 19, 2008 Learning objectives- Understand how scoring matrices are constructed. Workshop-Use different BLOSUM matrices in the Dotter.

Scoring Matrices June 19, 2008 Learning objectives- Understand how scoring matrices are constructed. Workshop-Use different BLOSUM matrices in the Dotter.

Practical Bioinformatics - HistoBasehisto.ucsf.edu/BMS270/BMS270_2015/slides/Slides08_Dynamic... · PAM (Dayho ) and BLOSUM matrices PAM1 matrix originally calculated from manual

Practical Bioinformatics - HistoBasehisto.ucsf.edu/BMS270/BMS270_2015/slides/Slides08_Dynamic... · PAM (Dayho ) and BLOSUM matrices PAM1 matrix originally calculated from manual

Improving the reactivity of phenylacetylene macrocycles ...€¦ · properties of PAM1 are reported in the literature [39]. PAM1 was used in this study as a control molecule because

Improving the reactivity of phenylacetylene macrocycles ...€¦ · properties of PAM1 are reported in the literature [39]. PAM1 was used in this study as a control molecule because

Scoring and heuristic methods for sequence alignmentrshamir/algmb/presentations/heuristic... · •Higher PAM and Lower BLOSUM for more different sequences . Log-odds •All matrices

Scoring and heuristic methods for sequence alignmentrshamir/algmb/presentations/heuristic... · •Higher PAM and Lower BLOSUM for more different sequences . Log-odds •All matrices

dkcsmolyan.com · paM1

dkcsmolyan.com · paM1

This lecture - trhvidsten · This lecture ¾Sequence alignment ... 1MB304: Discrete structures for bioinformatics II 10 ... −PAM −BLOSUM T.R. Hvidsten: ...

This lecture - trhvidsten · This lecture ¾Sequence alignment ... 1MB304: Discrete structures for bioinformatics II 10 ... −PAM −BLOSUM T.R. Hvidsten: ...

Blosum Substitution Matrix Pab

Blosum Substitution Matrix Pab

Construction of Substitution Matrices BLOSUM: BLOcks SUbstitution Matrix PAM: Point Accepted Mutations.

Construction of Substitution Matrices BLOSUM: BLOcks SUbstitution Matrix PAM: Point Accepted Mutations.

chemogenomics.med.utoronto.cachemogenomics.med.utoronto.ca/supplem… · XLS file · Web view · 2013-06-10'irc21' 'yor121c' 'erv41' 'npy1' 'pam1' 'yel023c' 'stf1' 'yal004w' 'snf4'

chemogenomics.med.utoronto.cachemogenomics.med.utoronto.ca/supplem… · XLS file · Web view · 2013-06-10'irc21' 'yor121c' 'erv41' 'npy1' 'pam1' 'yel023c' 'stf1' 'yal004w' 'snf4'

Comparing Protein Sequences Tutorial 4. Comparing Protein Sequences Substitution Matrices –PAM - Point Accepted Mutations –BLOSUM - Blocks Substitution.

Comparing Protein Sequences Tutorial 4. Comparing Protein Sequences Substitution Matrices –PAM - Point Accepted Mutations –BLOSUM - Blocks Substitution.

BLOSUM Scoring Matrices - IITKhome.iitk.ac.in/~rsankar/courses/lec04.pdfDr. R. Sankar, BSE 633 (2020) BLOSUM Scoring Matrices Derived from UNGAPPED alignments Based on observed amino

BLOSUM Scoring Matrices - IITKhome.iitk.ac.in/~rsankar/courses/lec04.pdfDr. R. Sankar, BSE 633 (2020) BLOSUM Scoring Matrices Derived from UNGAPPED alignments Based on observed amino