Position Weight Matrix From Sequence Alignment

Question

[Timtico]

Hello,

I use a Perl script to find a specific sequence, and as output I parse a fastafile containing the match sequence including a defined number of basepairs.

Now I want to do a multiple sequence alignment (e.g. ClustalW), but I want a position weight matrix as output, since for compatibility issues I need to create sequence using an R package. (instead of online tools such as weblogo)

Anyone knows a alignment tool (Bioperl, Bioconductor, online?) which gives me the matrix as output?

Regards

[brentp]

Duplicate? Consensus Sequence

Answer 1

[brentp]

You can create a position weight matrix with motility (python or c++). The interface is very simple so even if you don't use python, it should be straight-forward.

seqs = ['AGATAA', 'TGATAA', 'AGATAG']
pwm = motility.make_pwm(seqs)
print (pwm.max_score(), pwm.min_score())
# (11.1699250014, 0.0)
print pwm
#[[1.5849625007211563, 0.0, 0.0, 1.0],
# [0.0, 0.0, 2.0, 0.0],
# [2.0, 0.0, 0.0, 0.0],
# [0.0, 0.0, 0.0, 2.0],
# [2.0, 0.0, 0.0, 0.0],
# [1.5849625007211563, 0.0, 1.0, 0.0]]

[Timtico]

thanks for the answer, I'm not familiar with python however.. would like to keep working in R and Perl.

Answer 2

[hadasa]

Have a look at the BioStrings package in R. It is part of the Bioconductor. To install

source("http://www.bioconductor.org/biocLite.R"
 biocLite("Biostrings")

[Timtico]

nice, the consmat() function in the biostrings package seems to do the trick :)

[tiago211287]

Just an update. Now it is called: consensusMatrix() function.