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Needleman-Wunsch Alignment Method: Homework Tasks and Learning Objectives

This post outlines homework submissions, learning objectives, and steps to perform Needleman-Wunsch Global Alignment program. It covers how to fill matrices and perform traceback alignments using linear gap penalties.

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Needleman-Wunsch Alignment Method: Homework Tasks and Learning Objectives

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  1. 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.

  2. Three steps • Initialization • Matrix fill • Traceback

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

  4. Matrix fill

  5. Traceback

  6. W(L) = gLequation 5.1 where g is the cost of a single gap. Affine gap penalty W(L) = gopen + gext(L) equation 5.2 Total score = equation 5.3

  7. Modified N-W Global alignment with linear gap penalty Sequence 1: ADCDN (vertical sequence) Sequence 2: AWCN (horizontal sequence)

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