Global Alignment

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This document is from a lab manual for an introduction to bioinformatics course. It discusses lab exercise #5 on sequence alignment. The instructor's name is Syed Mohammad Lokman and it is for a class at Asian University for Women. The document includes diagrams explaining the concepts of matches, mismatches, and gaps in global sequence alignment.

Education

Lab#5: Sequence Alignment (Global)
Asian University For Women
BINF 2000: Introduction to Bioinformatics
(Lab - Fall 2022)
Syed Mohammad Lokman
Instructor
Asian University for Women

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BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

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BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

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BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

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BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

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BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

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BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

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BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

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BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)
Diagonal Horizontal Vertical
Match or
Mismatch
Gap

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BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)
Match or
Mismatch
Gap
Gap

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BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)
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BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

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BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

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BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

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BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

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BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

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BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

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BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

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BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

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BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

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BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)
Lab#5 Exercise:
Sequence Alignment

This series of predictable changes that occurs in a community over time is called ecological succession.In another words, Ecological succession is the change in species composition over time; that is, the replacement of one group of species by another group of species. There are two major types of ecological succession: primary succession and secondary succession. In primary succession, a site that is initially absent of species becomes colonized for the very first time. In secondary succession, a site that supports an existing assemblage of species experiences a disturbance that changes the composition of species. Both types of succession can occur in terrestrial and aquatic ecosystems. The first species to arrive and colonize the newly formed habitat are pioneer species. These early colonizers contribute nutrients to the soil through organic matter accumulation from decomposition. Some early successional plant species can fix atmospheric nitrogen and thereby increase nitrogen availability in the soil for other plants. As soil nutrients increase over succession it allows for the colonization of previously nutrient-limited species that were unable to establish initially. This facilitates the turnover in species composition over time. In terrestrial ecosystems, this compositional shift corresponds to a change in life forms and distinct species assemblages transitioning from small herbaceous plants, to shrubs, and ultimately to stands of trees over the course of succession. Secondary succession in terrestrial ecosystems can initiate after fire, tornadoes/ hurricanes, or humans disturb an already established plant community, removing most species but leaving the soil intact. The disturbance changes exposure of the habitat to sunlight, wind, and water that alters colonization and the assemblage trajectory of the new plant community. Some plant species may arrive to the disturbed site from

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Global Alignment

1. Lab#5: Sequence Alignment (Global) Asian University For Women BINF 2000: Introduction to Bioinformatics (Lab - Fall 2022) Syed Mohammad Lokman Instructor Asian University for Women

2. 2 BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

3. 3 BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

4. 4 BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

5. 5 BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

6. 6 BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

7. 7 BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

8. 8 BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

9. 9 BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd) Diagonal Horizontal Vertical Match or Mismatch Gap

10. 10 BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd) Match or Mismatch Gap Gap

11. 11 BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd) 1 2 3 4 5 6 7 8 9 10

12. 12 BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

13. 13 BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

14. 14 BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

15. 15 BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

16. 16 BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

17. 17 BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

18. 18 BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

19. 19 BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

20. 20 BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd)

21. 21 BINF 2000: Introduction to Bioinformatics (Lab) Syed Mohammad Lokman (syed.lokman@auw.edu.bd) Lab#5 Exercise: Sequence Alignment

Global Alignment

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