'Pairwise alignments' presentation slideshows

Multiple Sequence Alignment (MSA)

Multiple Sequence Alignment (MSA). Fig. from Boris Steipe U. of Toronto. Sequence relationships. Uses of MSA Technical difficulties Select sequences Select objective function Optimize the objective function Exact algorithms Progressive algorithms Iterative algorithms Stochastic

2.11k views • 100 slides

Multiple Alignment

Multiple Alignment. Outline. Introduction to Multiple Alignment Progressive Alignment Scoring Multiple Alignments Partial Order Alignment A- Bruijn Approach to Multiple Alignment. Section 1: Introduction to Multiple Alignment. Multiple Sequence Alignment (MSA).

1.1k views • 69 slides

Multiple Sequence Alignment

Multiple Sequence Alignment. Alignment can be easy or difficult. Easy. Difficult due to insertions or deletions (indels). Homology: Definition.

981 views • 64 slides

Multiple Sequences Alignment

Multiple Sequences Alignment. Ka-Lok Ng Dept. of Bioinformatics Asia University. Outline. Multiple sequence alignment (MSA) Progressive Alignment Profile Progressive Alignment (ClustalW) Scoring Multiple Alignments Entropy Sum of Pairs Alignment.

793 views • 47 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

Multiple Alignment

Multiple Alignment. Multiple Alignment versus Pairwise Alignment. Up until now we have only tried to align two sequences. Multiple Alignment versus Pairwise Alignment. Up until now we have only tried to align two sequences. What about more than two? And what for?.

466 views • 39 slides

CS 5263 Bioinformatics

511 views • 37 slides

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

497 views • 34 slides

Multiple Sequence Alignment

Multiple Sequence Alignment. BMI/CS 576 www.biostat.wisc.edu/bmi576.html Colin Dewey cdewey@biostat.wisc.edu Fall 2010. Multiple Sequence Alignment: Task Definition. Given a set of more than 2 sequences a method for scoring an alignment Do:

511 views • 32 slides

Position-Specific Iterated BLAST (PSI-BLAST)

Position-Specific Iterated BLAST (PSI-BLAST). CISC 4020 Bioinformatics Spring 2012 Department of Computer and Information Science. Position specific iterated BLAST: PSI-BLAST.

871 views • 30 slides

Multiple Alignment

Multiple Alignment. Anders Gorm Pedersen Molecular Evolution Group Center for Biological Sequence Analysis gorm@cbs.dtu.dk. CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS. CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS. Refresher: pairwise alignments. 43.2% identity; Global alignment score: 374

434 views • 29 slides

Multiple Alignments Motifs/Profiles

Multiple Alignments Motifs/Profiles. What is multiple alignment? HOW does one do this? WHY does one do this? What do we mean by a motif or profile?. Prev. reading: Ch 1-5 Assigned reading: Ch 6.4, 6.5, 6.6. BIO520 Bioinformatics Jim Lund. Information from Alignments.

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Computational Genomics Lecture #3a

Computational Genomics Lecture #3a. Multiple sequence alignment. Background Readings : Chapters 2.5, 2.7 in the text book, Biological Sequence Analysis , Durbin et al., 2001. Chapters 3.5.1- 3.5.3, 3.6.2 in Introduction to Computational Molecular Biology , Setubal and Meidanis, 1997.

379 views • 25 slides

Multiple Sequence Alignment

A - T. A G -. G T T. G G G. G T G. G - -. T - A. T T A. - - A. - T A. C C A. C C C. - G C. - G -. Possible alignment. Possible alignment. Multiple Sequence Alignment. S 1 = AGGTC. S 2 = GTTCG. S 3 = TGAAC. Multiple Sequence Alignment (cont).

526 views • 23 slides

Multiple Sequence Alignment

Multiple Sequence Alignment. Multiple Alignment versus Pairwise Alignment. Up until now we have only tried to align two sequences. What about more than two? And what for? A faint similarity between two sequences becomes significant if present in many

325 views • 22 slides

Multiple Alignment

Multiple Alignment. Anders Gorm Pedersen Molecular Evolution Group Center for Biological Sequence Analysis gorm@cbs.dtu.dk. Refresher: pairwise alignments. 43.2% identity; Global alignment score: 374 10 20 30 40 50

348 views • 22 slides

BNFO 240

BNFO 240. Usman Roshan. Last time. Traceback for alignment How to select the gap penalties? Benchmark alignments Structural superimposition BAliBASE. Database searching. Suppose we have a set of 1,000,000 sequences

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Low Copy Repeats in the Human Genome Implications for Genomic Structure

336 views • 18 slides

BNFO 602 Multiple sequence alignment

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

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Theoretical methods for predicting gene function II. predicting protein domains

Theoretical methods for predicting gene function II. predicting protein domains and their function from sequence analysis. S. Wodak, ULB Inter-university DEA/DES in Bioinformatics. The main steps. [3.1]. Predict domains. [3.2]. Predict function of individual domains. Family G

223 views • 11 slides