Protein database searches using compositionally adjusted substitution matrices
نویسندگان
چکیده
منابع مشابه
Fold-specific substitution matrices for protein classification
MOTIVATION Methods that focus on secondary structures, such as Position Specific Scoring Matrices and Hidden Markov Models, have proved useful for assigning proteins to families. However, for assigning proteins to an attribute class within a family these methods may introduce more free parameters than are needed. There are fewer members and there is less variability among sequences within a fam...
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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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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...
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ژورنال
عنوان ژورنال: FEBS Journal
سال: 2005
ISSN: 1742-464X,1742-4658
DOI: 10.1111/j.1742-4658.2005.04945.x