Hi all,
How to calculate the pairwise genetic distances between protein sequences in R? I have already calculated pairwise sequence identity and stored in excel file. I imported this excel file in to R. But I couldn't generate a distance matrix based on this file. I used dist.alignment function but I got an error like this
"Object of class 'alignment' expected" ? Please help me to solve this problem
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written
by
Sanju •
1 answer
Get your sequence file in either of the following formats
mase, clustal, msf, phylip, fasta
Then you can read this file into an Object of class alignment
library(seqinr)
myseqs <- read.alignment("mySeq.fasta", format = "fasta")
mat <- dist.alignment(myseqs, matrix = "identity")
dist.alignment() will calculate "pairwise Distances from Aligned Protein or DNA/RNA Sequences". The output matrix (mat) will look like
Langur Baboon Human Rat Cow
Baboon 0.3307189
Human 0.3750000 0.3307189
Rat 0.5448624 0.5077524 0.5376453
Cow 0.4921255 0.5448624 0.5590170 0.6495191
Horse 0.7071068 0.7071068 0.7015608 0.7015608 0.7342088
•
written
by
Yogesh Pandit •
@y2p actually my file is not an aligned file. It is a excel file. This file contains sequence identity data.for eg
1 2 3 4 5 6 7
1
2 11.1
3 11.1 100.0
4 11.1 100.0 100.0
5 18.2 11.1 11.1 11.1
6 21.7 11.1 11.1 11.1 100.0
7 22.2 11.1 11.1 11.1 44.4 44.4
8 80.0 20.0 20.0 20.0 80.0 80.0 100.0
How to generate distance matrix from this excel file based on sequence identity data? Which function I have to use for this?
@y2p. Actually my file is not an aligned file. It is an excel file which contains the percentage of sequence identity.My aim is to generate a distance matrix based on this data. That is distance= 100-sequence identity. which function I have to use for this?Do you have any idea?
@y2p. I have 300 sheets in excel file. Sequence identity data is in 9th column. I imported all sequence identity values from 300 sheets in to R using this code.
library(gdata)
myfile<-NULL;
for (i in 1:300) {
myfile[[i]]<-read.xls("C://Users//Desktop//mydata.xls",sheet=i,head=F)[,9]
}
myfile
Next I have to apply distance formula and to create a matrix. The formula is
distance = 100 - sequenceidentity.
Please help me
@vitis these are just squared root pairwise distances from similarity/identity matrices
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Try editing your question to include the code you are using, example input, and also the output of sessionInfo(). Also, be sure to read the help for the dist.alignment function.