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The Smith-Waterman algorithm is a dynamic programming algorithm used to perform sequence alignment, particularly in bioinformatics. It is an improvement over the Needleman-Wunsch algorithm, as it allo…
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This can be done with Needleman–Wunsch algorithm. Like the title mentions its an algorithm that allowed you to align protein or nucleotide sequences. This algorithm will be in its own file to follow t…
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The Smith-Waterman algorithm is a dynamic programming algorithm used to perform sequence alignment, particularly in bioinformatics. It is an improvement over the Needleman-Wunsch algorithm, as it allo…
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Create test to ensure that Needleman-Wunsch outputs accurate scores and alignment. Include proper documentation for users and collaborators.
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During a larger alignment job, my kernel dies. I attach the dataset I used in ZIP file:
[pickles.zip](https://github.com/althonos/pyopal/files/11582950/pickles.zip)
Reproducible snippet:
```
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https://en.wikipedia.org/wiki/Smith-Waterman_algorithm#Explanation
Smith-Waterman is a slight evolution of Needleman-Wunsch where the initial row and column weights are set to 0.
Smith-Waterman begi…
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Hi,
I know FAST-All is shortened to FASTA, but why is it called FAST? Is FAST an acronym, or is it just an adjective?
The 1985 paper has a note that says
"The algorithm used to calculate the …
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I temporarily copy-pasted the Needleman-Wunsch algorithm and adapted it to the Smith-Waterman algorithm.
Will need to abstract out the code that both of these pairwise alignments share with one ano…
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Being able to find a protein/test if it exists in the dna sequence is useful in DNA analyzing. I will implement it as an optional parameter to the CLI.
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Hello, the following algorithm is intended to use the Gotoh algorithm
aligner = PairwiseAligner() # for example
aligner.mode = 'global'
aligner.query_extend_gap_score = x
aligner.query_open_gap_…