In Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing Signals (link below) Gene Yao estimates the consensus sequences of 5' splice site. The author provides two versions of the sequence in figures 5 and 6.
I want to determine how strong is my 5' splice site sequence:
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I think that the closer my splice site sequence to the consensus one the more frequently the splisosome will bind to the site and the stronger my site will be. That is why I want to count some metric (distance) between the consensus sequence and my sequence. Is it possible to do that using only the information provided in the article?
http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.91.9713&rep=rep1&type=pdf
sure you can, e.g. using R packages in Bioconductor, e.g. the package TFBSTools. Can you program in R?
And what is the PWM of the binding site? Is there a matrix for the logo given somewhere in the article?
Unfortunately one has only the logos ... then you should magnify the logos and measure the heights - and calculate the proprotions for each positions with the length measures you can do from the logos. By that you can create yourself a pwm for each of the logos.
Once you have this, you can use the R package to calculate the similarity between your sequence and the pwm. If you don't know how to program this, I could help you. But the measuring you should do yourself. :)
Wow, measuring letter heights on a picture is a bit rough but totally valid idea. It turns out, there is even a tool for that:Article Logo2PWM: a tool to convert sequence logo to position weight matrix
Thank you, Gwang-Jin Kim!- Badges
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