title: Scores for sequence searches and alignments.
abstract: Every sequence comparison method requires a set of scores. For aligning protein sequences, substitution scores are based on models of amino acid conservation and properties, and matrices of these scores have substantially improved in recent years. Position-specific scoring matrices provide representations of sequence families that are capable of detecting subtle similarities. Comprehensive evaluations can effectively guide the choice of scores for sequence alignment and searching applications, including those that aid in the prediction of protein structures.
authors.affiliation: Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98104, USA. steveh@howard.fhcrc.org
authors.forename: S
authors.initials: S
authors.lastname: Henikoff
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry; D016208:Databases, Factual; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D012107:Research Design; D016415:Sequence Alignment; D015534:Trans-Activators / Q000737:chemistry; D014157:Transcription Factors / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; C058169:MetR protein, Bacteria; D015534:Trans-Activators; D014157:Transcription Factors; C070136:RbcR protein, Bacteria