'Substitution matrices' presentation slideshows

Comparing Two Protein Sequences

1.02k views • 76 slides

Comparing Two Protein Sequences

868 views • 75 slides

Comparing Two Protein Sequences

719 views • 71 slides

Lesson 3

698 views • 55 slides

Construction of Substitution matrices BLOSUM BLO CKS SU BSTITUTION M ATRIX PAM

Construction of Substitution matrices BLOSUM BLO CKS SU BSTITUTION M ATRIX PAM P OINT A CCEPTED M UTATIONS. Substitution matrices

865 views • 55 slides

Tutorial 2: Some problems in bioinformatics 1. Alignment pairs of sequences

Tutorial 2: Some problems in bioinformatics 1. Alignment pairs of sequences Database searching for sequences Multiple sequence alignment Protein classification 2. Phylogeny prediction (tree construction). Sources:

638 views • 51 slides

6.096 Algorithms for Computational Biology Lecture 2 BLAST & Database Search

6.096 Algorithms for Computational Biology Lecture 2 BLAST & Database Search. Manolis. Piotr Indyk. 1. 3. 2. Gene Finding. Sequence alignment. Database lookup. In Previous Lecture. DNA. BLAST and Database Search. Setup The BLAST algorithm BLAST extensions Substitutions matrices

675 views • 50 slides

Scores and substitution matrices in sequence alignment

624 views • 48 slides

Sequences are related

Sequences are related. Darwin: all organisms are related through descent with modification Related molecules have similar functions in different organisms. Phylogenetic tree based on ribosomal RNA: three domains of life. Sequences are related, II.

596 views • 45 slides

Database Searching:BLAST and FASTA

Database Searching:BLAST and FASTA. Biological Sequence Databases. NCBI Nucleotide GenBank, EMBL, DDBJ, GSDB, patent sequences Protein SwissProt, PIR, PRF, PDB (structural) PopSet GDB, FlyBase, OMIM, HGMD, MGD, GED There are other types of biological databases : EcoCyc, WIT/WIT2, others.

771 views • 44 slides

Protein homology I: Evolution and comparison of protein sequences

Protein homology I: Evolution and comparison of protein sequences. Biochem 565, Fall 2008 09/17/08 Cordes. Outline. Homology and kinds of homology Mutations and sequence conservation 3. Pairwise alignment--global vs. local 4. Sequence identity and homology

804 views • 42 slides

Tutorial 4 Substitution matrices and PSI-BLAST

Tutorial 4 Substitution matrices and PSI-BLAST. Agenda. Substitution Matrices PAM - Point Accepted Mutations BLOSUM - Blocks Substitution Matrix PSI-BLAST Cool story of the day: Why should we care about cellular fusion in worms?. Studying distant homologies.

382 views • 38 slides

Pairwise sequence alignments

Pairwise sequence alignments. Etienne de Villiers Adapted with permission of Swiss EMBnet node and SIB. Outline. Introduction Definitions Biological context of pairwise alignments Computing of pairwise alignments Some programs. Importance of pairwise alignments.

741 views • 36 slides

Introduction to Bioinformatics

Introduction to Bioinformatics. Alexandra M Schnoes Univ. California San Francisco Alexandra.Schnoes@ucsf.edu. What is Bioinformatics?. Intersection of Biology and Computers Broad field Often means different things to different people Personal Definition:

543 views • 33 slides

1-month Practical Course Genome Analysis Lecture 3: Residue exchange matrices

C. E. N. T. E. R. F. O. R. I. N. T. E. G. R. A. T. I. V. E. B. I. O. I. N. F. O. R. M. A. T. I. C. S. V. U. 1-month Practical Course Genome Analysis Lecture 3: Residue exchange matrices Centre for Integrative Bioinformatics VU (IBIVU)

473 views • 28 slides

Tutorial 4 Substitution matrices and PSI-BLAST

Tutorial 4 Substitution matrices and PSI-BLAST. Agenda. Why study distant homologies? Substitution Matrices PAM - Point Accepted Mutations BLOSUM - Blocks Substitution Matrix PSI-BLAST Cool story of the day: Why should we care about cellular fusion in worms?. How proteins evolve.

1.14k views • 27 slides

Modeling Molecular Substitution

Modeling Molecular Substitution Von Bing Yap Statistics Department, UC Berkeley yapvb@stat.berkeley.edu Variations on a theme Human genome project furnishes sequences from a few individuals, but is relevant to all of us: we are very similar. We are also slightly different: polymorphisms.

851 views • 26 slides

Burkhard Morgenstern Grundlagen der Bioinformatik Subsitutionsmatrizen SS 07

Burkhard Morgenstern Grundlagen der Bioinformatik Subsitutionsmatrizen SS 07. Substitution matrices. All protein alignment programs depend on similarity scores s(a,b) Similarity score s(a,b) for amino acids a and b is based on probability p a,b of substitution a -> b

243 views • 15 slides

Calculating substitution matrices

Calculating substitution matrices.

162 views • 10 slides

Position-Specific Substitution Matrices

Position-Specific Substitution Matrices. PSSM. A regular substitution matrix uses the same scores for any given pair of amino acids regardless of where in the protein they are.

176 views • 10 slides