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Question: Identify in tandem repeats with Bioconductor
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gravatar for Vinicius Henrique da Silva
15 months ago by
Brazil

I would like to identify the regions with repeated patterns in a given genome. Let's say that I need to identify [TA]n regions, were 'n' is a variable number of repeats.

I thought in a loop to resolve the problem, however, it will take a long time and will produce redundant regions. Thus, I would like to know if there is a efficient way to analyze that.

library("Biostrings")
G = readDNAStringSet("any.fa")

seqAll <- seq(from =1 , to =1000, by=1) 
ali <- NULL

for(k in 1:length(seqAll)){
nx <- seqAll[k]

patx <- paste(rep("AT",nx), sep="", collapse="")

ali[k] <- vmatchPattern(DNAString(patx), G, max.mismatch=0)
}
ADD COMMENTlink modified 14 months ago by Hervé Pagès ♦♦ 13k • written 15 months ago by Vinicius Henrique da Silva20
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gravatar for Hervé Pagès
14 months ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:

Hi Vinicius,

You might want to check this post for a more efficient approach:

    A: Is there any package helps finding Tandem Repeats ?

Cheers,

H.

ADD COMMENTlink written 14 months ago by Hervé Pagès ♦♦ 13k
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