The compositional adjustment of amino acid substitution matrices
نویسندگان
چکیده
منابع مشابه
The compositional adjustment of amino acid substitution matrices.
Amino acid substitution matrices are central to protein-comparison methods. In most commonly used matrices, the substitution scores take a log-odds form, involving the ratio of "target" to "background" frequencies derived from large, carefully curated sets of protein alignments. However, such matrices often are used to compare protein sequences with amino acid compositions that differ markedly ...
متن کاملAmino acid substitution matrices.
The BLOSUM (BLOck SUbstitution Matrices) matrices were derived by Steven and Jorja Henikoff in 1992 1. They were based on a much larger data set than the PAM matrices, and used conserved local alignments or “blocks,” rather than global alignments of very closely related sequences. In order to account for different degrees of sequence divergence, the Henikoffs used clustering rather than an expl...
متن کاملAmino Acid Substitution Matrices
• Biophysical properties of residues: Amino acids differ in size and charge. Some are acidic, some are basic, some have aromatic side chains. Generally, replacement of an amino acid with another amino acid with similar properties is less likely to break the protein or cause dramatic changes in function than replacement with an amino acid with different properties. A substitution matrix should r...
متن کاملAmino Acid Substitution Matrices Tuesday
• Biophysical properties of residues: Amino acids differ in size and charge. Some are acidic, some are basic, some have aromatic side chains. Generally, replacement of an amino acid with another amino acid with similar properties is less likely to break the protein or cause a dramatic change in function than replacement with an amino acid with different properties. A substitution matrix should ...
متن کاملAmino acid substitution matrices from protein blocks.
Methods for alignment of protein sequences typically measure similarity by using a substitution matrix with scores for all possible exchanges of one amino acid with another. The most widely used matrices are based on the Dayhoff model of evolutionary rates. Using a different approach, we have derived substitution matrices from about 2000 blocks of aligned sequence segments characterizing more t...
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ژورنال
عنوان ژورنال: Proceedings of the National Academy of Sciences
سال: 2003
ISSN: 0027-8424,1091-6490
DOI: 10.1073/pnas.2533904100