Question: Delete certain nucleotide positions in multiple nucleotide alignment
0
gravatar for mariasv1
10 weeks ago by
mariasv10
mariasv10 wrote:

Hi all,

I have a large multiple nucleotide alignment, and I need to delete specific nucleotide positions from each sequence (basically I need to delete several columns of nucleotides). Someone familiar with a sufficient way to do this?

I was thinking to read an alignment as data.frame in R, and then delete selected columns. But I am having troubles to separate nucleotides by columns.

what I have now:

mydata<-readDNAStringSet("myalignmet.fas")
names<-names(mydata)
sequence<-paste(mydata)
ptid<-names
df<-data.frame(names, sequence)
df$sequence<-as.character(df$sequence)
df2$sequence<-strsplit(df2$sequence, " ")

I am getting a column df$sequence as c("A", "C", "G", "T", ...).

Thanks in advance, Maria

alignment R • 154 views
ADD COMMENTlink modified 10 weeks ago by WouterDeCoster36k • written 10 weeks ago by mariasv10

How do you determine which to delete? Do you know the column numbers? I have edited your title to make it more specific.

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by WouterDeCoster36k

Yes, I have specific nucleotide positions which I want to delete (they associate with resistance)

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by mariasv10

There probably is a way to do this in R, but I'd do it in Python. Do you know any Python?

ADD REPLYlink written 10 weeks ago by WouterDeCoster36k

column wise deletion from an MSA can be done in bioedit mariasv1

ADD REPLYlink written 10 weeks ago by cpad011211k
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