Alignment methods

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Alignment methods October 16, 2012 Return Quiz 1 today Return homework on Thursday. Homework from last week due on Thursday Learning objectives- Needleman Wunsch Global Alignment program. New Homework exercises #5 and #6 from Chapter 5.

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Alignment methods. October 16, 2012 Return Quiz 1 today Return homework on Thursday. Homework from last week due on Thursday Learning objectives- Needleman Wunsch Global Alignment program. New Homework exercises #5 and #6 from Chapter 5. Three steps. Initialization Matrix fill Traceback. - PowerPoint PPT Presentation

Transcript of Alignment methods

Page 1: Alignment methods

Alignment methodsOctober 16, 2012Return Quiz 1 todayReturn homework on Thursday.Homework from last week due on ThursdayLearning objectives- Needleman Wunsch Global Alignment program.New Homework exercises #5 and #6 from Chapter 5.

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Three steps

Initialization

Matrix fill

Traceback

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Alignment A Sequence 1: ADCDN-R-CKCRWP Sequence 2: AWC-NDRQCLCR-P Score: 10101010101101Total Score: 8Alignment B Sequence 1: ADC-DNR-CKCRWP Sequence 2: AWCND-RQCLCR-P Score: 10101010101101Total Score: 8

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A W C N D R Q C L C R P

A 1

D 1

C 1 1 1

D 1

N 1

R 1 1

C 1 1 1

K

C 1 1 1

R 1 1

W 1

P 1

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Matrix fill

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Traceback

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W(L) = gL equation 5.1where g is the cost of a single gap.

Affine gap penaltyW(L) = gopen + gext(L) equation 5.2

Total score = equation 5.3

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Modified N-W Global alignment with linear gap penalty

Sequence 1: ADCDN (vertical sequence)Sequence 2: AWCN (horizontal sequence)

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Multiple sequence alignment. Multiple sequence alignment: outline [1] Introduction to MSA Exact methods Progressive (ClustalW) Iterative (MUSCLE) Consistency.

Multiple sequence alignment. Multiple sequence alignment: outline [1] Introduction to MSA Exact methods Progressive (ClustalW) Iterative (MUSCLE) Consistency.

Pioneer ACO Alignment and Financial Reconciliation Methods ...Pioneer ACO Alignment and Financial Reconciliation Methods 7 March 26, 2014 Ver. 9.1 through the 2 nd thquarter of CY2012

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Threedimensional Alignment Methods for the HERA ... · PDF fileThreedimensional Alignment Methods for the ... lapping lines measured with an E2-Theodolite ... Threedimensional Alignment

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Sequence Alignment Methods and Algorithms

Sequence Alignment Methods and Algorithms

Martijn Vermaat Department of Human Genetics Center for ......Alignment methods Sequence alignment Assembly vs alignment Alignment methods Common issues Platform specifics Software

Martijn Vermaat Department of Human Genetics Center for ......Alignment methods Sequence alignment Assembly vs alignment Alignment methods Common issues Platform specifics Software

Large-scale multiple sequence alignment and phylogeny ...tandy/warnow-mage-paper.pdfTable 1. Table of methods for large-scale multiple sequence alignment estimation. We show methods

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Genome Alignment. Alignment Methods Needleman-Wunsch (global) and Smith- Waterman (local) use dynamic programming Guaranteed to find an optimal alignment.

Genome Alignment. Alignment Methods Needleman-Wunsch (global) and Smith- Waterman (local) use dynamic programming Guaranteed to find an optimal alignment.

Chapter 6: Multiple Sequence Alignment - FH Münster · Multiple sequence alignment: methods How do we know which program to use? There are benchmarking multiple alignment datasets

Chapter 6: Multiple Sequence Alignment - FH Münster · Multiple sequence alignment: methods How do we know which program to use? There are benchmarking multiple alignment datasets

Structural Alignment Methods with Applications to Geospatial

Structural Alignment Methods with Applications to Geospatial

Next Generation Sequencing, Assembly, and Alignment Methods

Next Generation Sequencing, Assembly, and Alignment Methods

Decentralized coordination methods for beam alignment and ...

Decentralized coordination methods for beam alignment and ...

Computational Methods for the Alignment and Score-Informed ...

Computational Methods for the Alignment and Score-Informed ...

Multiple Sequence Alignment (III) and Evolution/Phylogenetic methods

Multiple Sequence Alignment (III) and Evolution/Phylogenetic methods

Pioneer ACO Alignment and Financial Reconciliation Methods · 2020. 3. 9. · Pioneer ACO Alignment and Financial Reconciliation Methods 1 . ... 29 Addendum C: Technical ... BY1/AY2:

Pioneer ACO Alignment and Financial Reconciliation Methods · 2020. 3. 9. · Pioneer ACO Alignment and Financial Reconciliation Methods 1 . ... 29 Addendum C: Technical ... BY1/AY2:

Alignment-free Sequence Analysis Methods · Alignment-free Sequence Analysis Methods Hector Espitia hspitia@gatech.edu PhD Student | Bioinformatics | Jordan Lab. Computational Genomics

Alignment-free Sequence Analysis Methods · Alignment-free Sequence Analysis Methods Hector Espitia [email protected] PhD Student | Bioinformatics | Jordan Lab. Computational Genomics

Alignment methods June 26, 2007 Learning objectives- Understand how Global alignment program works. Understand how Local alignment program works.

Alignment methods June 26, 2007 Learning objectives- Understand how Global alignment program works. Understand how Local alignment program works.

Chapter 6. Multiple sequence alignment methods

Chapter 6. Multiple sequence alignment methods

Pioneer ACO Alignment and Financial Reconciliation Methods · Pioneer ACO Alignment and Financial Reconciliation ... Pioneer ACO Alignment and Financial Reconciliation Methods ...

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Sequence Alignment II K-tuple methods Statistics of alignments.

Sequence Alignment II K-tuple methods Statistics of alignments.

Alignment methods Introduction to global and local sequence alignment methods Global : Needleman-Wunch Local : Smith-Waterman Database Search BLAST FASTA.

Alignment methods Introduction to global and local sequence alignment methods Global : Needleman-Wunch Local : Smith-Waterman Database Search BLAST FASTA.