Browsing by Author "Sverdlov, Sophie"

There are many software packages for modeling transcription factors’ binding affinities, both for prediction and classification, and for visualization. In this thesis I survey several methods and evaluate their fitness for discriminating between positive and negative sequences in the data set: • BaMM method • PMMs method • Slim method • Log-odds Sequence Logos method • CircularLogo method • InMoDe method • TFFMs method • DWM method I first compared the packages based on a review of the papers in which they are presented. Based on that comparison, I selected the three that seemed the most promising for the application, and evaluated their fitness and ease of use.