Motif Extraction Using R Package?

Question

[p2011001]

I am a biologist and struggling to extract motif information from a number of protein sequences using a bioinformatics approach in R. Is there any such packages to extract motif information from a number of protein sequence to classify the proteins based to motifs.

Thanks in advance

[Pappu]

MEME is the best.

Answer 1

[Ashwin]

Hi,

I don’t know of any specific package to solve your problem, but what you can do is use the biomaRt package in R.

Get the user guide here http://www.bioconductor.org/packages/2.13/bioc/vignettes/biomaRt/inst/doc/biomaRt.pdf

If you have a set of protein sequence - map them to its Uniprot identifier (or any other protein identifier). This should be possible using biomaRt package or any other tool that you might prefer for mapping.

using the getBM( ) function in BiomaRt, you can identify domains Id for each of your proteins from Uniprot, Interpro or /and PFAM.

Now simply sort the vector containing your domain ID along with the protein ID and you will have proteins sharing similar motifs together.

Since many proteins might have multiple motifs matching you could do some more "data tricks" and keep/sort proteins with maximum number of similar motifs together.

Since your question is quite general and I cant give you an example specific solution, however biomaRt will definitely help you !!

Cheers Ashwin