Calculate pairwise distance for 3000 small sequences
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7.5 years ago
ekal ▴ 20

I have a .fasta with 3000 ascensions, each of which is 10 bases long. I need to calculate the alignment score between each pair of sequences - that's 3000^2 comparisons. Using R or python, what's the best way to go about doing this? Technical details like code snippets are particularly helpful.

Thanks!!

fasta sequence blast • 2.7k views
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This post has some tips and example python code: Massive Pairwise Comparison Using Biopython

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This sounds like an interesting challenge for a 100 lines C program. ;)

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You can use biostrings package with R. It is samplest methode I think.see

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