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Old 08-04-2019, 07:56 PM   #1
Meyana
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Location: Japan

Join Date: Sep 2017
Posts: 37
Default Pair-wise comparison of DNA sequences

Hi,
I'm hoping someone can help me with what I presume to be a simple task, but one I couldn't find a solution to myself

I have a table of DNA sequences with two columns, like this:

Seq1 Seq2
AAGGTTCC GAGGTTCA
GGTTCCAA TTAACTAC
...

Now, I would like to do a pairwise comparison of these sequences and get a "similarity score" out of it...
I.e. comparing Seq1 and Seq2 on a per-row basis, not across columns or an Seq1 to Seq2 comparison of all sequences.

If an R package is available I would be extremely happy, but other options are of course more than welcome

Thanks!


EDIT
I should mention that all sequences will be of the same length.
The exact length is undecided, 12 at the shortest, 30 at the longest. It will depend on how results look.

Last edited by Meyana; 08-05-2019 at 05:26 PM.
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