Table 6 Tested substitution matrices
Matrix | Reference | Description |
|---|---|---|
Evolutionary matrices | ||
PAM 30, 60, 120, 250 | Dayhoff et al. [1] | Evolutionary model of point substitutions |
Blosum45, 50, 62 | Henikoff et al. [2] | Series based on the alignment of segments of related sequences from protein families grouped into blocks |
Gonnet250 | Gonnet et al. [5] | Matrix based on substitutions in protein families on an extended database for long evolutionary distances |
Gonnet_p | Vogt et al. [6] | Later modification of Gonnet250 |
Optima | Kann et al. [7] | Detection of differences between homologues and non-homologues for a large evolutionary distance |
VTML250 | Muller et al. [3] | Improved evolutionary model based on maximal likelihood method (for distant homologue detection) |
MIQS | Yamada et al. [8] | Data derived on the basis of principal component analysis of the previously known matrices (Blosum, VTML, Benner) |
Pfasum 50, 100 | Keul et al. [4] | Model based on modern data covering a large and diverse sequence space. |
Matrix based on Dirichlet mixture model | ||
Crooks | Crooks et al. [9] | The model takes into account the difference in the dynamics of substitutions depending on the time of evolution. |
Evolutionary matrices for special protein families | ||
CCF53 | Brick et al. [10] | Search for homologues in families of related proteins, taking into account the bias of the amino acid composition characteristic for proteins of two species of the genus Plasmodium. |
MOLLI60 | Lemaitre et al. [11] | General method for constructing matrices focused on a certain bias of amino acid composition, based on the example of bacteria proteins of the Mollicutes class. |
Matrices based on the structural alignment | ||
Johnson | Johnson et al. [12] | Obtained by calculating the substitutions of amino acid residues in the structural alignment of proteins from homologous families with a low level of sequence identity. |
Prlic | Prlic et al. [13] | Obtained on the basis of superposition of pairs of proteins having a similar structure, but low sequence identity. |
Blake | Blake et al. [14] | Based on structural superposition data, taking into account differences in arrays of amino acid residues substitutions for distant and closely related homologs. |
Genetic code matrix | ||
Benner | Benner et al. [16] | Based on the number of nucleotide substitutions required for a given amino acid substitution. |
Contacts energy matrix | ||
Miyazawa | Miyazawa et al. [15] | Based on the assessment of the distribution of contacts in three-dimensional protein structure. |