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This means that one may use Jordan forms that only exist over a larger field to determine whether the given matrices are similar. In the definition of similarity, if the matrix P can be chosen to be a permutation matrix then A and B are permutation-similar; if P can be chosen to be a unitary matrix then A and B are unitarily equivalent.
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Similarity Matrix of Proteins (SIMAP) is a database of protein similarities created using volunteer computing. [ 1 ] [ 2 ] It is freely accessible for scientific purposes. SIMAP uses the FASTA algorithm to precalculate protein similarity, while another application uses hidden Markov models to search for protein domains .
Two similar matrices represent the same linear map, but with respect to a different basis; unitary equivalence corresponds to a change from an orthonormal basis to another orthonormal basis. If A and B are unitarily equivalent, then tr AA * = tr BB *, where tr denotes the trace (in other words, the Frobenius norm is a unitary invariant).
Matrix congruence is an equivalence relation. Matrix congruence arises when considering the effect of change of basis on the Gram matrix attached to a bilinear form or quadratic form on a finite-dimensional vector space: two matrices are congruent if and only if they represent the same bilinear form with respect to different bases.
This is the same matrix as defines a Givens rotation, but for Jacobi rotations the choice of angle is different (very roughly half as large), since the rotation is applied on both sides simultaneously. It is not necessary to calculate the angle itself to apply the rotation. Using Kronecker delta notation, the matrix entries can be written:
Not every square matrix is similar to a companion matrix, but every square matrix is similar to a block diagonal matrix made of companion matrices. If we also demand that the polynomial of each diagonal block divides the next one, they are uniquely determined by A , and this gives the rational canonical form of A .
So for real matrices similar by some real matrix , consimilarity is the same as matrix similarity. Like ordinary similarity, consimilarity is an equivalence relation on the set of n × n {\displaystyle n\times n} matrices, and it is reasonable to ask what properties it preserves.