Question: Calculate the score of sequence from Position-specific scoring matrix (PSSM)
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gravatar for howenwy2
3 months ago by
howenwy20
howenwy20 wrote:

Hi, I have a question about calculating PSSM score

I have a Position-specific scoring matrix (PSSM) and 400 fasta sequeces about 18bp length PSSM I know that I can calculate the score based on the position of ATCG; however, I couldn't calculate in manually because I have so many sequences here.

I was wandering if I can calculate it with R codes or unix codes.

Thank you

ADD COMMENTlink written 3 months ago by howenwy20
1

Resources page at Gary Stormo's lab has all kinds of resources dedicated to this problem - I think patser and consensus may be doing exactly what you want. Morpheus may be useful as well.

ADD REPLYlink written 3 months ago by Mensur Dlakic6.0k

Thank you so much for your help, but those websites didn't work for me.

https://www.cmbl.uga.edu//software/motloc.html

I use this website to predict the promoter region of my bacteria. The input data is a bacterial genome sequence from NCBI and a set of aligned motifs. The output was nice with both the predict promoter sequence and the gene near that region. And there are 400 sequences. And I also have a Matrix of PSSM and 400 promoter sequences; however, I don't have the score of individual sequence.

How can I calculate the score from a given matrix?

ADD REPLYlink modified 3 months ago • written 3 months ago by howenwy20
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