Multiple Alignment

Multiple Alignment. Outline. Dynamic Programming in 3-D Progressive Alignment Profile Progressive Alignment (ClustalW) Scoring Multiple Alignments Entropy Sum of Pairs Alignment Partial Order Alignment (POA) A-Bruijin (ABA) Approach to Multiple Alignment.

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Multiple Sequence Alignment

An Introduction to Bioinformatics. Multiple Sequence Alignment. AIMS. To introduce the different approaches to multiple sequence alignment. To identify criteria for selecting a multiple sequence alignment program. OBJECTIVES. To select an appropriate multiple sequence alignment program.

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Multiple Alignment

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Multiple Sequence Alignment

Multiple Sequence Alignment. Index-based local alignment. ……. Dictionary: All words of length k (~10) Alignment initiated between words of alignment score  T (typically T = k) Alignment: Ungapped extensions until score below statistical threshold Output:

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Multiple Sequence Alignment

Multiple Sequence Alignment. Definition. Given N sequences x 1 , x 2 ,…, x N : Insert gaps (-) in each sequence x i , such that All sequences have the same length L Score of the global map is maximum. Applications. Scoring Function: Sum Of Pairs . Definition: Induced pairwise alignment

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Multiple Alignment

Multiple Alignment. Modified from Tolga Can’s lecture notes (METU). Outline. Problem definition Can we use Dynamic Programming to solve MSA? Progressive Alignment ClustalW Scoring Multiple Alignments Entropy Sum of Pairs (SP) Score. Multiple Alignment versus Pairwise Alignment.

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Multiple Alignment –

Multiple Alignment –. Υλικό βασισμένο στο κεφάλαιο 1 4 του βιβλίου : Dan Gusfield, Algorithms on Strings, Trees and Sequences, Cambridge University Press. Three c ο mm ο n representations. There are three common kinds of family representations that come from multiple string comparison:

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Multiple alignment

Multiple alignment. June 29, 2007 Learning objectives- Review sequence alignment answer and answer questions you may have. Understand how the E value may be altered by changing your search criteria. Understand usefulness of multiple sequence alignment. Become familiar with Clustal W.

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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?.

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Multiple Sequence Alignment

Multiple Sequence Alignment. Multiple Alignment- First pair. Align the two most closely-related sequences first.

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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).

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Multiple Sequence Alignment

Multiple Sequence Alignment. Kun-Mao Chao ( 趙坤茂 ) Department of Computer Science and Information Engineering National Taiwan University, Taiwan WWW: http://www.csie.ntu.edu.tw/~kmchao. MSA. Multiple sequence alignment (MSA).

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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

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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

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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).

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Multiple Sequence Alignment

Multiple Sequence Alignment. Mult-Seq-Align allows to detect similarities which cannot be detected with Pairwise-Seq-Align methods. Detection of family characteristics. Three questions: 1. Scoring Computation of Mult-Seq-Align. Family representation. Multiple Sequence Alignment.

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Multiple Alignment

Multiple Alignment. Stuart M. Brown NYU School of Medicine. Pairwise Alignment. The alignment of two sequences (DNA or protein) is a relatively straightforward computational problem. The best solution seems to be an approach called Dynamic Programming. Dynamic Programming.

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Multiple Sequence Alignment

Multiple Sequence Alignment. Julie Thompson Laboratory of Integrative Bioinformatics and Genomics IGBMC, Strasbourg, France julie@igbmc.fr. Multiple Sequence Alignment. Introduction: what is a multiple alignment? Multiple alignment construction Traditional approaches: optimal, progressive

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Multiple alignment

One of the most essential tools in molecular biology Finding highly conserved subregions or embedded patterns of a set of biological sequences Conserved regions usually are key functional regions, prime targets for drug developments Estimation of evolutionary distance between sequences

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Multiple Alignment

Multiple Alignment. Outline. Problem definition Can we use Dynamic Programming to solve MSA? Progressive Alignment ClustalW Scoring Multiple Alignments Entropy Sum of Pairs (SP) Score. Multiple Alignment versus Pairwise Alignment. Up until now we have only tried to align two sequences.

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Multiple-Alignment

Multiple-Alignment. 藍永倫、陳婕妤、文國煒、劉宗灝、戴邦炘. Reference.

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Multiple Sequence Alignment

Multiple Sequence Alignment. Algorithms in Computational Biology Spring 2006. Most of the slides were created by Dan Geiger and Ydo Wexler and edited by Itai Sharon, other created by Itai Sharon. S 1 =AGGTC. S 2 =GTTCG. S 3 =TGAAC. Possible alignment. Possible alignment. A - T. A G -.

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