[BioC] Count differences between sequences

[Patrick Aboyoun]

Erik,
Could you provide more details on your data? How long are each of the strings and how many strings do you have? Also, do you need the entire N x N distance matrix for downstream analysis or are you just looking for closest relatives?


Patrick



On 3/25/10 2:29 PM, erikwright at comcast.net wrote:
> Hello all,
>
>
> I have a large DNAStringSet and I am trying to calculate its distance matrix. My DNAStrings are equal width and they are already aligned.
>
>
> I have tried using the stringDist() function, but it is very slow for large DNAStringSets. Is there a way to quickly calculate the number of differences between two DNAString instances?
>
>
> For example, let's say I have two DNAStrings: "ACAC" and "ACAG". I would like to know if their is a function other than stringDist() that will tell me the distance between them is 1.
>
>
> Thanks in advance for any help.
>
>
> - Erik
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