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Module 3 Session.2 Practical Assignment-Lucy Nakabazzi

This document provides instructions for an assignment on pairwise sequence alignment. It introduces local versus global alignment and demonstrates how choosing different parameters for the Smith-Waterman and Needleman-Wunsch algorithms can significantly impact the alignment results. Students are asked to perform sample local and global alignments of protein sequences using various online tools while adjusting parameters, and observe how it affects metrics like identity percentage and gap penalties. They also complete interactive games to learn about sequence alignment and dynamic programming.

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lucy kabazzi
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207 views4 pages

Module 3 Session.2 Practical Assignment-Lucy Nakabazzi

This document provides instructions for an assignment on pairwise sequence alignment. It introduces local versus global alignment and demonstrates how choosing different parameters for the Smith-Waterman and Needleman-Wunsch algorithms can significantly impact the alignment results. Students are asked to perform sample local and global alignments of protein sequences using various online tools while adjusting parameters, and observe how it affects metrics like identity percentage and gap penalties. They also complete interactive games to learn about sequence alignment and dynamic programming.

Uploaded by

lucy kabazzi
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as DOCX, PDF, TXT or read online on Scribd
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Introduction to Bioinformatics online course: IBT

Practical Assignment
Module name: Sequence alignment theory and applications
Session name: Pairwise Sequence Alignment
Trainer: Jonathan Kayondo, Sonal Henson
Participant: <Lucy Nakabazzi>
Date: <29th August, 2022>

Pairwise Sequence Alignment


Introduction
Sequence alignment is a complex biological task with several strategies and programs to pick
from. The methods usually require intelligent use of several variables in the programs.
Dynamic programming helps with finding optimal sequence alignments.

This exercise demonstrates the usefulness of the local alignment in bioinformatics, and also
what can go wrong if you are not careful in choosing your parameters. We also look at the
dynamic programming applications in the Needleman-Wunsch algorithm.

Tools used in this session

Uniprot - www.uniprot.org
EMBOSS Water – www.ebi.ac.uk/Tools/psa/emboss_water/
EMBOSS Needle - www.ebi.ac.uk/Tools/psa/emboss_needle/
TeachEnG - http://teacheng.illinois.edu/

Please note

 Hand-in information If you are formally enrolled in the IBT course, please upload
your completed assignment to the Vula ‘Assignments’ tab. Take note of the final
hand-in date for each assignment, which will be indicated on Vula.

Task 1: Local vs Global alignment and choosing the correct parameters.

Task 1: instructions
The local alignment finds regions of local similarity. It is implemented trough Smith–
Waterman (but other also) algorithm. It has many purposes, and just some of them are
finding motifs, finding one sequence within another, search sequence databases, etc.
Introduction to Bioinformatics online course: IBT

Using the Smith-Waterman algorithm we will make a local pairwise alignment of an


unknown sequence to the ACV synthetase of Penicilliumchrysogenum and investigate the
effect of adjusting the alignment parameters on the output.

1. Go to www.uniprot.org and download the sequence for ACV synthetase of


Penicillium chrysogenum (accession number: P26046).
2. Download unknown_sequence.fasta from Vula -> Practical Assignments -> Module 3
Session 2
3. Go to www.ebi.ac.uk/Tools/psa/emboss_water/ to make your alignment.
4. Upload or paste the P. chrysogenum sequence in the first box and the unknown
sequence in the second box.
5. Click ‘Submit’ to execute the alignment.
6. Click on ‘View Alignment File’ and save your alignment output in a text file.
7. Go back to the alignment submission page and repeat step 4.
8. Click on ‘More options’ under Step 2 and set the Gap Open and Gap Extend to
minimum.
9. Submit your alignment.
10. How does your alignment from step 5 and step 9 compare in terms of alignment
score, % identity, % similarity, gaps, and the extent (positions) of alignment of the
two sequences?

11. Now use the Needleman-Wunsch algorithm for global pairwise alignment to align
the two sequences from steps 1 and 2. You can use the EBI tool Needle for that
(http://www.ebi.ac.uk/Tools/psa/emboss_needle/)
12. Follow steps 4-6 to submit the alignment.
13. How does your alignment compare with that from step 6?
14. Repeat steps 8 and 9, this time on the Needle program.
15. How does the alignment compare to that from step 12 (using default parameters)?
16. This exercise demonstrates the usefulness of the local alignment in bioinformatics,
and also what can go wrong if you are not careful in choosing your parameters.

Task 1: participant’s answer


<
10. Alignment from step 5
Length: 830
Identity: 517/830 (62.3%)
Similarity: 628/830 (75.7%)
Gaps: 15/830 (1.8%)
Score: 2590.5
Positions of alignment: 2
Alignment from step 9
Introduction to Bioinformatics online course: IBT
Gap open minimum=1
Gap extend minimum=0.0005
Length: 3757
Identity: 517/3757 (13.8%)
Similarity: 628/3757 (16.7%)
Gaps: 2940/3757 (78.3%)
Score: 2587.5
Positions of alignment: 2

13.
Length: 3757
Identity: 517/3757 (13.8%)
Similarity: 628/3757 (16.7%)
Gaps: 2940/3757 (78.3%)
Score: 2587.5
Positions of alignment: 2

14.Length: 3776
Identity: 675/3776 (17.9%)
Similarity: 760/3776 (20.1%)
Gaps: 2978/3776 (78.9%)
Score: 3337.0
15.
The % identity, % similarity, gaps, and the extent (positions) of alignment of the two
sequences are quite similar and relatable, although the overall alignment score is not the
same.
16.

>

Task 2: Dynamic programming

Task 2: instructions

1. Go to TeachEnG (http://teacheng.illinois.edu/) and play the Sequence Alignment


game. Click on the ‘Play’ button on the right of the page. Try all the three levels. Test
the effect of adjusting the parameters on the overall score.
Introduction to Bioinformatics online course: IBT
2. Similarly, play the Needleman-Wunsch algorithm game. Fill out the dynamic
programming matrix. Refer to the Instructional Material for help on how to play the
game.

Task 2: participant’s answer


<

>

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