1 / 14

Alignment methods

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.

faolan
Download Presentation

Alignment methods

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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)

More Related