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I have two sequences and I need to perform sequence alignment to determine all possible sequence alignments. I have created the matrix and managed to find 16 alignments.

I wanted to understand if I had correctly approached this because I need to provide all possible alignment sequences and then provide the best alignment sequence/sequences out of all the ones found, however, all my found sequences have a score of -9. I have provided 2 sequences I found below, and all 16 found sequences can be found in a pastebin link below since it made the post quite large.

I was wondering if someone could help me understand if I may have gone wrong or if I am missing some sequences since all of them have a score of -9. I do not think I have gone wrong during the matrix creation phase but I am unsure. I have asked for help from my tutor however he has been quite rude and reluctant to explain/help so I have decided to turn to the community for help and guidance. Would appreciate any insight into this. Thanks in advance.

Sequence strings:

ggaatggmeeff

gatge

Alignment matrix

enter image description here

Found sequences: Sequences with score.

1.  Score: -9
G   G   A   A   T   G   G   M   E   E   F   F

G   -   -   A   T   -   G   -   -   E   -   -

2. Score: -9
G   G   A   A   T   G   G   M   E   E   F   F

-   G   -   A   T   -   G   -   -   E   -   -
Krellex
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1 Answers1

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Your alignment score is low because your sequences are short and one is twice as long as the other. This inescapably introduces gaps in the alignment leading to a low alignment score. This alignment with a -9 score is still the optimal global alignment accordting to the Needleman Wunsch algorithm.

Pallie
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  • Thanks for the reply! When determining sequences, if a sequence does not go from the most bottom right to the most top left, is this still a potential sequence, just not the best one? I have been tasked to find ALL possible sequences but since all my sequence scores are -9, I find myself confused. – Krellex Apr 12 '22 at 17:40
  • In needleman wunsch you always start your traceback at the bottom right cell in your scoring matrix, there is only one optimal alignment. Starting the traceback in any other cell will give an alternative alignment, but that is not how needleman wunsch is used. – Pallie Apr 13 '22 at 08:00
  • Ah ok. You mention there is only one optimal alignment, how do you determine this? I thought this was determined using the score however all my alignments have a score of -9 which would suggest their equally as optimal as each other? – Krellex Apr 13 '22 at 08:02
  • Take a look at https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm#Tracing_arrows_back_to_origin – Pallie Apr 13 '22 at 08:07