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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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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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develop smith waterman function:
- Should input 2 sequences, gap penalty, match score, mismatch scores
- output the score of their similarity
- Output the alignment of the two sequences:
Ex:
…
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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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Any plans to add Smith-Waterman algorithm?
Or perhaps the same outcome can be achieved using existing functionality?
Than you
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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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Dear Zhao mengyao,
Not a issue, but a question
Is a local alignment like Smith-Waterman typically/always considered to be symmetric?
I.e. is score of alignment(s,t) the same as score of alignmen…
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Hello.
I was trying to assemble a genome with mira, and the process got killed for some reason (probably the server ran out of memory). When I tried to resume the assembly from a checkpoint by using…
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Hi,
Thank you for making this nice tool.
I tried to install it by using pip, but it was an error.
```
FileNotFoundError: [Errno 2] No such file or directory: 'fasta35': 'fasta35'
```
I tried…