While handling a database, I have a single transcription factor sequence, but the database gives multiple Position Weight Matrices (PWMs) for the DNA site said TF binds. This is because the different PWMs are measured with different methods and from different sources. How do I handle and represent both PWMs in a single PWM? Should I choose the PWM from the more "accurate" method, or simply take the average of each position?
Hey there! Dealing with multiple PWMs can be tricky. If you have access to the original studies or sources of the PWMs, it might be worth looking into their validation and accuracy. If one is clearly more reliable than the other, you could use that one for your analysis. Alternatively, you could try combining the PWMs by taking the average of each position. However, keep in mind that this could lead to a loss of specificity and sensitivity in predicting binding sites. It may also be worth exploring other methods for combining PWMs, such as using machine learning algorithms. Ultimately, it's important to carefully consider the strengths and limitations of each approach and choose the one that is best suited to your specific needs and goals.
Looking for a more accurate PWM isn't an option, I have a database with over 15k sequence-to-PWM comparisons. I think I'll stick with taking the average for each position. Some duplicate PWMs have differing lengths and positions, though. How should I deal with that?
- Badges
- Science method