Question: Position Weight Matrix in R or Python
2
gravatar for esantosh10
4.7 years ago by
esantosh1030
Germany
esantosh1030 wrote:

Hello All,

I would like to create a position weight matrix in R or Python for some peptide sequences . I found that there are packages in R to create a position weight matrix for gene sequences(ATGC) like Biostrings but was difficult to find them for proteins/peptides. Any suggestions?

peptide pwm matrix • 7.2k views
ADD COMMENTlink modified 3.4 years ago by kamil_cygan20 • written 4.7 years ago by esantosh1030
2
gravatar for madk00k
4.7 years ago by
madk00k330
Heidelberg
madk00k330 wrote:

Biopython allows to create Position Weight Matrices using motifs module:

http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec244

As far as I know, there are know constrains for the alphabet, so it could polypeptide.

 

ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by madk00k330
2
gravatar for kamil_cygan
3.4 years ago by
kamil_cygan20
United States
kamil_cygan20 wrote:

Actually, you can create PSSM for amino acids in a similar manner as for DNA/RNA sequences.

library(Biostrings)
sequences <- c("ERLRELETKIGSLQEDLC","CERLRELETKIGSLQEDL","ERLRECLETKIGSLQEDL")
string_set <- AAStringSet(sequences)
PSSM <- consensusMatrix(string_set, as.prob = TRUE)
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by kamil_cygan20
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