Maximum Entropy Weighting of Aligned Sequencesof Proteins or

In a family of proteins or other biological sequences like DNA the various subfamilies are often very unevenly represented. For this reason a scheme for assigning weights to each sequence can greatly improve performance at tasks such as database searching with prooles or other consensus models based on multiple alignments. A new weighting scheme for this type of database search is proposed. In a statistical description of the searching problem it is derived from the maximum entropy principle. It can be proved that, in a certain sense, it corrects for uneven representation. It is shown that nding the maximum entropy weights is an easy optimization problem for which standard techniques are applicable.