Question: Calculate pairwise distance for 3000 small sequences
0
gravatar for ekal
2.8 years ago by
ekal10
ekal10 wrote:

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!!

blast sequence fasta • 1.2k views
ADD COMMENTlink modified 2.8 years ago by Biostar ♦♦ 20 • written 2.8 years ago by ekal10

This post has some tips and example python code: Massive Pairwise Comparison Using Biopython

ADD REPLYlink written 2.8 years ago by Tonor420

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

ADD REPLYlink written 2.8 years ago by kloetzl1.0k

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

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Macherki M E120
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