![]() The match = 1, mismatch = –1, fixed-gap-penalty system is doomed to result in low alignment scores in this case: the best possible score is 5 x 1 (matches) + 7 x –2 (gaps) = –9. There is another fundamental defect here, which arises from the scoring system used. I can think of no justification for this. But the trackback shown, as well as having instances where the highest scoring cell has been missed, has 9 cases where the trackback is to two cells with different scores. However the problem with the Needleman and Wunsch trackback is that in this algorithm each cell should trackback to the single highest-scoring cell preceding it - if there are two of the same score a random choice is made. Although, memory limitations permitting, one could program this, the algorithm is not designed to find lower scores (and I find it hard to see the demand for such). This operation is not performed in any programatic implementations of the algorithm of which I am aware. Although it is possible in general to trace alternative trackbacks of the same score manually, I do not see any in this example. Such a trackback is designed to find one of what are generally several possible alignments that have the highest score using a specific scoring matrix and gap penalties (different scoring systems can give different alignments). The display presented looks at first sight like a trackback for a global alignment using the Needleman and Wunsch dynamic programming algorithm. The reason for doubting this is that the number of possible alignments with no restraint imposed will vary from very large to astronomical, depending on the length of the sequences. If the former, I doubt that the wording expresses the request correctly, even though this is repeated in the question as “My goal is to find all sequences and not just the optimal (highest?) ones”. It is not clear whether this need is that determined by a course assignment or the poster’s mathematical imagination. The poster writes “I need to perform sequence alignment to determine all possible sequence alignments”. 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. My goal is to find all sequences and not just the optimal ones. ![]() I do not think I have gone wrong during the matrix creation phase but I am unsure. 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. The sequences I have found I have placed in this pastebin link: Sequences since I did not want to make the post too large. 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 created the matrix and managed to find 16 alignments. I have two sequences and I need to perform sequence alignment to determine all possible sequence alignments.
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