'Gap penalties' presentation slideshows

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FCH 532 Lecture 8

FCH 532 Lecture 8

FCH 532 Lecture 8. Exam on Friday Chapter 7. Sequence alignments. An alignment score (AS) is used to determine if there is any relationship. 10 for every identity except Cys which scores 20 Subtract 25 for every gap.

By Pat_Xavi
(155 views)

Sequence comparison: Significance of similarity scores

Sequence comparison: Significance of similarity scores

Sequence comparison: Significance of similarity scores. Genome 559: Introduction to Statistical and Computational Genomics Prof. William Stafford Noble. One-minute responses. I'm confused as to when I should parentheses versus brackets.

By apollo
(240 views)

Basic String Alignment

Basic String Alignment

Basic String Alignment. Probability theory and statistics String alignment problem Basic string alignment algorithms. Author: Roel Wijgers email: rwijgers@cs.uu.nl. Probability Theory. Conditional chance: P(A|B) = P(A /\ B) / P(B) Independence of A and B: when P(A /\ B) = P(A)P(B).

By bess
(127 views)

Sequence comparison: Score matrices

Sequence comparison: Score matrices

Sequence comparison: Score matrices. http://faculty.washington.edu/jht/GS559_2013/. Genome 559: Introduction to Statistical and Computational Genomics Prof. James H. Thomas. FYI - informal inductive proof of best alignment path.

By saul
(65 views)

BNFO 602 Multiple sequence alignment

BNFO 602 Multiple sequence alignment

BNFO 602 Multiple sequence alignment. Usman Roshan. Optimal pairwise alignment.

By alton
(95 views)

Bioinformatics

Bioinformatics

Bioinformatics. Prof. William Stafford Noble Department of Genome Sciences Department of Computer Science and Engineering University of Washington thabangh@gmail.com. One-minute responses. Be patient with us. Go a bit slower. It will be good to see some Python revision.

By landen
(102 views)

BIOMETRICS

BIOMETRICS

BIOMETRICS. Module Code: CA641 Week 11- Pairwise Sequence Alignment. Outline. Why should one do sequence comparison ? Dynamic programming alignment algorithms global alignment (Needleman- Wunsch ) local alignment (Smith-Waterman ) Heuristic alignment algorithms : FASTA , BLAST

By kynton
(196 views)

Sequence Comparison

Sequence Comparison

Sequence Comparison. Pair-wise Similarities. Sequence Comparison. Graphical Alignments Compare DotPlot Pairwise alignments BestFit Gap. Similarity vs. Homology. Similarity Two sequences which resemble each other Can be measured Degrees of similarity exist Homology

By iola
(160 views)

Biological Sequence Comparison / Database Homology Searching

Biological Sequence Comparison / Database Homology Searching

Biological Sequence Comparison / Database Homology Searching. Database Homology Searching. Use algorithms to increase efficiency and to provide a mathematical basis for searches which can be translated into statistical significance

By zeke
(91 views)

A Pairwise Alignment Algorithm Which Favors Clusters of Blocks

A Pairwise Alignment Algorithm Which Favors Clusters of Blocks

A Pairwise Alignment Algorithm Which Favors Clusters of Blocks. Original : Joel Lipschultz Modified by : Shiuan-Wen Chen Date : Dec. 29, 2005. Abstract.

By calida
(69 views)

Space Efficient Alignment Algorithms and Affine Gap Penalties

Space Efficient Alignment Algorithms and Affine Gap Penalties

Space Efficient Alignment Algorithms and Affine Gap Penalties. Dr. Nancy Warter-Perez. Outline. Algorithm complexity Complexity of dynamic programming alignment algorithms Memory efficient algorithms Hirschberg’s Divide and Conquer algorithm Affine gap penalty. Algorithm Complexity.

By patsy
(213 views)

BIOINFORMATICS Sequences #2

BIOINFORMATICS Sequences #2

BIOINFORMATICS Sequences #2. Mark Gerstein, Yale University GersteinLab.org/courses/452 (last edit in fall '05). Basic Alignment via Dynamic Programming Suboptimal Alignment Gap Penalties Similarity (PAM) Matrices Multiple Alignment Profiles, Motifs, HMMs Local Alignment

By whitney
(105 views)

MBoMS Genomics of Model Microbes Lab 4: Multiple sequence alignment

MBoMS Genomics of Model Microbes Lab 4: Multiple sequence alignment

MBoMS Genomics of Model Microbes Lab 4: Multiple sequence alignment. Multiple Sequence Alignments. Your next task will be to create multiple sequence alignments This is one of the most challenging steps in the study of molecular evolution

By juro
(86 views)

Alignment principles and homology searching using (PSI-)BLAST Jaap Heringa

Alignment principles and homology searching using (PSI-)BLAST Jaap Heringa

Alignment principles and homology searching using (PSI-)BLAST Jaap Heringa Centre for Integrative Bioinformatics VU (IBIVU) http://ibivu.cs.vu.nl. Bioinformatics. “Nothing in Biology makes sense except in the light of evolution” (Theodosius Dobzhansky (1900-1975))

By xanto
(144 views)

Pairwise Alignment Global & local alignment

Pairwise Alignment Global & local alignment

Pairwise Alignment Global & local alignment. Anders Gorm Pedersen Molecular Evolution Group Center for Biological Sequence Analysis. Sequences are related. Darwin: all organisms are related through descent with modification => Sequences are related through descent with modification

By olin
(152 views)

Wellcome Trust Workshop Working with Pathogen Genomes Module 6 Phylogeny

Wellcome Trust Workshop Working with Pathogen Genomes Module 6 Phylogeny

Wellcome Trust Workshop Working with Pathogen Genomes Module 6 Phylogeny. Phylogeny. Phylogeny refers to the ancestry of a biological lineage, but is also synonymous with phylogenetic tree Taxonomy began by grouping taxa together based on morphology at various structural levels

By geona
(171 views)

1-month Practical Course Genome Analysis 2008 Lecture 3: Profiles: representing sequence alignment

1-month Practical Course Genome Analysis 2008 Lecture 3: Profiles: representing sequence alignment

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 2008 Lecture 3: Profiles: representing sequence alignment Centre for Integrative Bioinformatics VU (IBIVU)

By natala
(187 views)

Computational Biology or Bioinformatics

Computational Biology or Bioinformatics

Computational Biology or Bioinformatics. ability to rapidly sequence DNA has led to large databases development of new algorithms data analysis and interpretation similar concepts also applied to epidemiological databases genetic epidemiology evolutionary genetics

By minya
(125 views)

Lecture 3: Scoring Matrices and Multiple Sequence Alignment BMI/IBGP 730

Lecture 3: Scoring Matrices and Multiple Sequence Alignment BMI/IBGP 730

Lecture 3: Scoring Matrices and Multiple Sequence Alignment BMI/IBGP 730. Kun Huang Department of Biomedical Informatics Ohio State University. Review of sequence alignment Scoring matrices Multiple sequence alignment Tools and examples. 18. 3. 20. 5. 25. B. 2. A. 11.

By mahsa
(187 views)

Barking Up the Wrong Treelength

Barking Up the Wrong Treelength

Kevin Liu, Serita Nelesen, Sindhu Raghavan, C. Randal Linder, and Tandy Warnow IEEE TCCB 2009. Barking Up the Wrong Treelength. Minimizing Treelength. Generalized Input: set S of sequences and a function f(s, s') for the edit distance between sequences s and s'

By wolfe
(67 views)

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