Has anyone prepared a script in R to plot the profiles of DOPE score in accordance with the alignment of compared structures?
- description: http://salilab.org/modeller/tutorial/basic.html
If u could provide all sample input files of DOPE alignment that we input in R, then probably I could help u. Post the sample files (TvLDH.profile).
1bdmA.profile and TvLDH.profile - these are the energetical profiles of both proteins
This is the alignment of those two proteins - the plot of profiles should be in accordance with this alignment
This is the final plot (note, that there are gaps in the curves - it due to gaps in alignment)
and this is the script in python - this script should run also in R, but it doesn't.
a little help:
#read data from profile files
prof1=read.table("1bdmA.profile", header=TRUE)
prof2=read.table("TvLDH.profile", header=TRUE)
# make 1 common table
allprofiles=cbind(prof1$"TOTAL", prof2$"TOTAL")
#plot profiles
matplot(dane, type="l", lty=1, lwd=2)
but this is without alignment.
#read the file, skip first 7 lines
data=read.table("1bdmA.profile",skip=7);
# Plot resid(column1) and total score(column 42), type of plot="l" (line plot)
plot(data$V1,data$V42,type="l",xlab="Resid",ylab="Total DOPE Score");
# Save the plot
savePlot("DopePlot.png");
As i have no idea how u want to plot, so i have plotted a basic line plot between resid and total dope score
I want to plot both curves (1bdmA.profile and TvLDH.profile) together in one plot (as an example DOPE_plot.jpg) in accordance to sequence alignment (TvLDH-1bdmA.ali) of both proteins.
OK, no problem. If you have no idea how to do it, I'll try in a free time and post it here.
Thanks ;)
Its seems simple to do. We need to first map both target and template residue wise and then map this alignment back to dope score. Same here ( ;) I too will do when get free time). Please post if u do :)
How do you generate the pharmacophore models of protein structures taking into consideration the active sites of these proteins... any free software??
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