Entering edit mode
4.0 years ago
howenwy2
•
0
Hi, I have a question about calculating PSSM score
I have a Position-specific scoring matrix (PSSM) and 400 fasta sequeces about 18bp length 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
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.
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?