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DOC: acks section & fix binary mention in first ex
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fedarko committed Sep 3, 2023
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Expand Up @@ -23,7 +23,7 @@ s1 = "AGCAGGAGATAAACCTGT"
s2 = "AGCAGGTTATCTACCTGT"
k = 3

# Create the matrix (the "binary" parameter means we'll distinguish forward,
# Create the matrix (setting binary=False means we'll distinguish forward,
# reverse-complementary, and palindromic matching k-mers from each other)
m = wotplot.DotPlotMatrix(s1, s2, k, binary=False)

Expand Down Expand Up @@ -141,6 +141,17 @@ cd wotplot
pip install -e .[dev]
```

## Acknowledgements

The small example given above, and my initial implementation of an algorithm
for computing dot plots, were based on
[_Bioinformatics Algorithms_](https://www.bioinformaticsalgorithms.org)
(Compeau & Pevzner).

The idea of using suffix arrays to speed up dot plot computation is not new; it
is also implemented in
[Gepard](https://academic.oup.com/bioinformatics/article/23/8/1026/198110).

## Contact

Feel free to [open an issue](https://github.com/fedarko/wotplot/issues) if you
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