title: Maximum entropy weighting of aligned sequences of proteins or DNA.
abstract: 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 profiles 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 finding the maximum entropy weights is an easy optimization problem for which standard techniques are applicable.
authors.affiliation: Laboratory of Molecular Biology, Cambridge, England.
authors.forename: A
authors.initials: A
authors.lastname: Krogh
authors.forename: G
authors.initials: G
authors.lastname: Mitchison
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D016384:Consensus Sequence; D017124:Conserved Sequence; D004247:DNA / Q000737:chemistry*; D016208:Databases, Factual; D006801:Humans; D008390:Markov Chains; D008433:Mathematics; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D013816:Thermodynamics
chemical_list: D011506:Proteins; D004247:DNA