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SeqMatchNW-P |
| Input | |
| Target sequence | Place your query file with protein sequences in FASTA format. |
| Query sequence(s) | Place input file with one ore more protein sequences in FASTA format. |
| Output | |
| Result | Name of the output file. |
| Format | Output format:
List of alignment blocks coordinates (default) List of alignment blocks coordinates and blocks sequences Output alignment General alignment information General alignment information, blocks list and alignment |
| Sort blocks | Sort regions of homology for "List of alignment blocks coordinates" value of "Output format" option :
Don't sort (default) Incremental sort by coordinates on target Incremental sort by coordinates on Query Decremental sort by alignment block score Decremental sort by alignment block weight Decremental sort by alignment block length |
| Flank type | Flank type:
Length - Output for given amount of symbols in flank of alignment block. All - unlimited flank |
| Position number | Print additional strings with position number for target and query strings. |
| Numeration Offset | Numeration Offset:
Target - Given value will be added to taget sequence numeration on output Query - Given value will be added to query sequence numeration on output |
| Homology | Output symbol as separator lines between target and query, each line separator position shows similarity between target and query positions |
| Gap | Use given simbol to print output gaps |
| Tailing Gap | Use given simbol to print output flanking gaps in profile output, default: '-' |
| Line Tearing | String used for displaying of big gaps in alignment. |
| Output string | Output for given amount of symbols in each line. |
| Unalignment info | Produce output information for sequences where no similarity found. |
| Perfect only | Output perfect and near-perfect alignment. |
| Graphic data | Name of the output binary t-file. |
| Preprocessing | |
| Remove | |
| PolyA | Remove polyA tail from taget sequence. It is may be useful if target sequence is mRNA or EST. |
| PolyT | Remove polyT head from taget sequence. It is may be useful if target sequence is complemented mRNA or EST. |
| Trailing N | Remove trailing N symbols from both ends of target sequence. |
| Cut Sequence | |
| Start | Search in target sequence from given position |
| End | Search in target sequence to given position. "0" - get to end |
| Apply to chain | Search in target sequence is applied to reverse chain. |
| Options | |
| Scoring matrix | Select one of the standard pre-defined matrix. |
| Tail gap | Tail gap:
Alignment with tail gaps penalties Alignment without tail gaps penalties |
| Gap Initiation penalty | Gap Initiation penalty in average match units. |
| Gap Continuation penalty | Gap Continuation penalty in average match units. |
| Match score | Match score, if Single-score scoring chosen (Similarity scoring only). |
| Mismatch penalty | Mismatch penalty, if Single-score scoring chosen. |
| Score method | Scoring methods for whole alignment:
No scoring the alignment (default) Score of alignment is the probability of the best block in alignment Score of alignment is the probability of the summ of all blocks of alignment Blast-like scoring method (in SD units) Blast-like scoring method (in probability units) |
| Threshold | If alignment has score less then given value then alignment is not printed. |
| Fine adjustment | Fine adjustment of alignment blocks ends. |
| Alternate variants | Produce given best alternate variants of alignments. Value "All" - all possible variants |
| Non-overlapped variants | Produce given non-overlapped variants of alignments. Value "All" - all possible variants |
| Different variants | Produce given different variants of alignments. "All" - all possible variants |
| Local alignment | Produce local alignment. Split alignment to several local alignments. |
| Split diagonal recursively | Split diagonal recursively (if possible). |
| Target | |
| By length | Alignment region on target sequence does not exeed given length. |
| By multiplier | Alignment region on target sequence does not exeed length of query sequence multiplied to N (N - is floting poin number). |
| By range | Alignment region on target sequence does not exeed length of query sequence plus N. |
| Query | |
| By length | Alignment region on query sequence does not exeed given length. |
| By multiplier | Alignment region on query sequence does not exeed length of query sequence multiplied to N (N - is floting poin number). |
| By range | Alignment region on query sequence does not exeed length of query sequence plus N. |
| Translation table | Select translation table (Bacterial is default). |
Description of pre-defined matrix
| ALTS910101 |
The PAM-120 matrix (Altschul, 1991)
LIT:1713145 PMID:2051488 Altschul, S.F. Amino acid substitution matrices from an information theoretic perspective J. Mol. Biol. 219, 555-565 (1991) |
| BENS940101 |
Log-odds scoring matrix collected in 6.4-8.7 PAM (Benner et al., 1994)
LIT:2023094 PMID:7700864 Benner, S.A., Cohen, M.A. and Gonnet, G.H. Amino acid substitution during functionally constrained divergent evolution of protein sequences Protein Engineering 7, 1323-1332 (1994) * extrapolated to 250 PAM |
| BENS940102 |
Log-odds scoring matrix collected in 22-29 PAM (Benner et al., 1994)
LIT:2023094 PMID:7700864 Benner, S.A., Cohen, M.A. and Gonnet, G.H. Amino acid substitution during functionally constrained divergent evolution of protein sequences Protein Engineering 7, 1323-1332 (1994) * extrapolated to 250 PAM |
| BENS940103 |
Log-odds scoring matrix collected in 74-100 PAM (Benner et al., 1994)
LIT:2023094 PMID:7700864 Benner, S.A., Cohen, M.A. and Gonnet, G.H. Amino acid substitution during functionally constrained divergent evolution of protein sequences Protein Engineering 7, 1323-1332 (1994) * extrapolated to 250 PAM |
| BENS940104 |
Genetic code matrix (Benner et al., 1994)
LIT:2023094 PMID:7700864 Benner, S.A., Cohen, M.A. and Gonnet, G.H. Amino acid substitution during functionally constrained divergent evolution of protein sequences Protein Engineering 7, 1323-1332 (1994) * extrapolated to 250 PAM |
| CSEM940101 |
Residue replace ability matrix (Cserzo et al., 1994)
LIT:2022066 PMID:7966267 Cserzo, M., Bernassau, J.-M., Simon, I. and Maigret, B. New alignment strategy for transmembrane proteins J. Mol. Biol. 243, 388-396 (1994) * Diagonal elements are missing. * We use 1 as diagonal elements. |
| DAYM780301 |
Log odds matrix for 250 PAMs (Dayhoff et al., 1978)
R
Dayhoff, M.O., Schwartz, R.M. and Orcutt, B.C. A model of evolutionary change in proteins In "Atlas of Protein Sequence and Structure", Vol.5, Suppl.3 (Dayhoff, M.O., ed.), National Biomedical Research Foundation, Washington, D.C., p.352 (1978) |
| FEND850101 |
Structure-Genetic matrix (Feng et al., 1985)
LIT:1107900 PMID:6100188 Feng, D.F., Johnson, M.S. and Doolittle, R.F. Aligning amino acid sequences: comparison of commonly used methods J. Mol. Evol. 21, 112-125 (1985) |
| FITW660101 |
Mutation values for the interconversion of amino acid pairs (Fitch, 1966)
PMID:5917736 Fitch, W.M. An improved method of testing for evolutionary homology J. Mol. Biol. 16, 9-16 (1966) |
| GEOD900101 |
Hydrophobicity scoring matrix (George et al., 1990)
PMID:2314281 George, D.G., Barker, W.C. and Hunt, L.T. Mutation data matrix and its uses Methods Enzymol. 183, 333-351 (1990) |
| GONG920101 |
The mutation matrix for initially aligning (Gonnet et al., 1992)
LIT:1813110 PMID:1604319 Gonnet, G.H., Cohen, M.A. and Benner, S.A. Exhaustive matching of the entire protein sequence database Science 256, 1443-1445 (1992) |
| GRAR740104 |
Chemical distance (Grantham, 1974)
LIT:2004143 PMID:4843792 Grantham, R. Amino acid difference formula to help explain protein evolution Science 185, 862-864 (1974) |
| HENS920101 |
BLOSUM45 substitution matrix (Henikoff-Henikoff, 1992)
LIT:1902106 PMID:1438297 Henikoff, S. and Henikoff, J.G. Amino acid substitution matrices from protein blocks Proc. Natl. Acad. Sci. USA 89, 10915-10919 (1992) * matrix in 1/3 Bit Units |
| HENS920102 |
BLOSUM62 substitution matrix (Henikoff-Henikoff, 1992)
LIT:1902106 PMID:1438297 Henikoff, S. and Henikoff, J.G. Amino acid substitution matrices from protein blocks Proc. Natl. Acad. Sci. USA 89, 10915-10919 (1992) * matrix in 1/3 Bit Units |
| HENS920103 |
BLOSUM80 substitution matrix (Henikoff-Henikoff, 1992)
LIT:1902106 PMID:1438297 Henikoff, S. and Henikoff, J.G. Amino acid substitution matrices from protein blocks Proc. Natl. Acad. Sci. USA 89, 10915-10919 (1992) * matrix in 1/3 Bit Units |
| JOHM930101 |
Structure-based amino acid scoring table (Johnson-Overington, 1993)
LIT:1923112 PMID:8411177 Johnson, M.S. and Overington, J.P. A structural basis for sequence comparisons An evaluation of scoring methodologies J. Mol. Biol. 233, 716-738 (1993) |
| JOND920103 |
The 250 PAM PET91 matrix (Jones et al., 1992)
LIT:1814076 PMID:1633570 Jones, D.T., Taylor, W.R. and Thornton, J.M. The rapid generation of mutation data matrices from protein sequences CABIOS 8, 275-282 (1992) |
| JOND940101 |
The 250 PAM transmembrane protein exchange matrix (Jones et al., 1994)
LIT:2006072 PMID:8112466 Jones, D.T., Taylor, W.R. and Thornton, J.M. A mutation data matrix for transmembrane proteins FEBS Lett. 339, 269-275 (1994) |
| KOLA920101 |
Conformational similarity weight matrix (Kolaskar-Kulkarni-Kale, 1992)
LIT:1806109 PMID:1538389 Kolaskar, A.S. and Kulkarni-Kale, U. Sequence alignment approach to pick up conformationally similar protein fragments J. Mol. Biol. 223, 1053-1061 (1992) |
| LEVJ860101 |
The secondary structure similarity matrix (Levin et al., 1986)
LIT:1210126 PMID:3743779 Levin, J.M., Robson, B. and Garnier, J. An algorithm for secondary structure determination in proteins based on sequence similarity FEBS Lett. 205, 303-308 (1986) |
| LUTR910101 |
Structure-based comparison table for outside other class (Luthy et al., 1991)
LIT:1712085 PMID:1881879 Luthy, R., McLachlan, A.D. and Eisenberg, D. Secondary structure-based profiles: Use of structure-conserving scoring tables in searching protein sequence databases for structural similarities Proteins 10, 229-239 (1991) |
| LUTR910102 |
Structure-based comparison table for inside other class (Luthy et al., 1991)
LIT:1712085 PMID:1881879 Luthy, R., McLachlan, A.D. and Eisenberg, D. Secondary structure-based profiles: Use of structure-conserving scoring tables in searching protein sequence databases for structural similarities Proteins 10, 229-239 (1991) |
| LUTR910103 |
Structure-based comparison table for outside alpha class (Luthy et al., 1991)
LIT:1712085 PMID:1881879 Luthy, R., McLachlan, A.D. and Eisenberg, D. Secondary structure-based profiles: Use of structure-conserving scoring tables in searching protein sequence databases for structural similarities Proteins 10, 229-239 (1991) |
| LUTR910104 |
Structure-based comparison table for inside alpha class (Luthy et al., 1991)
LIT:1712085 PMID:1881879 Luthy, R., McLachlan, A.D. and Eisenberg, D. Secondary structure-based profiles: Use of structure-conserving scoring tables in searching protein sequence databases for structural similarities Proteins 10, 229-239 (1991) |
| LUTR910105 |
Structure-based comparison table for outside beta class (Luthy et al., 1991)
LIT:1712085 PMID:1881879 Luthy, R., McLachlan, A.D. and Eisenberg, D. Secondary structure-based profiles: Use of structure-conserving scoring tables in searching protein sequence databases for structural similarities Proteins 10, 229-239 (1991) |
| LUTR910106 |
Structure-based comparison table for inside beta class (Luthy et al., 1991)
LIT:1712085 PMID:1881879 Luthy, R., McLachlan, A.D. and Eisenberg, D. Secondary structure-based profiles: Use of structure-conserving scoring tables in searching protein sequence databases for structural similarities Proteins 10, 229-239 (1991) |
| LUTR910107 |
Structure-based comparison table for other class (Luthy et al., 1991)
LIT:1712085 PMID:1881879 Luthy, R., McLachlan, A.D. and Eisenberg, D. Secondary structure-based profiles: Use of structure-conserving scoring tables in searching protein sequence databases for structural similarities Proteins 10, 229-239 (1991) |
| LUTR910108 |
Structure-based comparison table for alpha helix class (Luthy et al., 1991)
LIT:1712085 PMID:1881879 Luthy, R., McLachlan, A.D. and Eisenberg, D. Secondary structure-based profiles: Use of structure-conserving scoring tables in searching protein sequence databases for structural similarities Proteins 10, 229-239 (1991) |
| LUTR910109 |
Structure-based comparison table for beta strand class (Luthy et al., 1991)
LIT:1712085 PMID:1881879 Luthy, R., McLachlan, A.D. and Eisenberg, D. Secondary structure-based profiles: Use of structure-conserving scoring tables in searching protein sequence databases for structural similarities Proteins 10, 229-239 (1991) |
| MCLA710101 |
The similarity of pairs of amino acids (McLachlan, 1971)
PMID:5167087 McLachlan, A.D. Tests for comparing related amino-acid sequences cytochrome c and cytochrome c551 J. Mol. Biol. 61, 409-424 (1971) * (RR 9.) |
| MCLA720101 |
Chemical similarity scores (McLachlan, 1972)
PMID:5023183 McLachlan, A.D. Repeating sequences and gene duplication in proteins J. Mol. Biol. 64, 417-437 (1972) |
| MIYS930101 |
Base-substitution-protein-stability matrix (Miyazawa-Jernigan, 1993)
LIT:1913158 PMID:8506261 Miyazawa, S. and Jernigan, R.L. A new substitution matrix for protein sequence searches based on contact frequencies in protein structures Protein Engineering 6, 267-278 (1993) |
| MIYT790101 |
Amino acid pair distance (Miyata et al., 1979)
LIT:0601606 PMID:439147 Miyata, T., Miyazawa, S. and Yasunaga, T. Two types of amino acid substitutions in protein evolution J. Mol. Evol. 12, 219-236 (1979) |
| MOHR870101 |
EMPAR matrix (Mohana Rao, 1987)
LIT:1304091 PMID:3570667 Mohana Rao, J.K. New scoring matrix for amino acid residue exchanges based on residue characteristic physical parameters Int. J. Peptide Protein Res. 29, 276-281 (1987) |
| NIEK910101 |
Structure-derived correlation matrix 1 (Niefind-Schomburg, 1991)
LIT:1713140 PMID:2051484 Niefind, K. and Schomburg, D. Amino acid similarity coefficients for protein modeling and sequence alignment derived from main-chain folding angles J. Mol. Biol. 219, 481-497 (1991) |
| NIEK910102 |
Structure-derived correlation matrix 2 (Niefind-Schomburg, 1991)
LIT:1713140 PMID:2051484 Niefind, K. and Schomburg, D. Amino acid similarity coefficients for protein modeling and sequence alignment derived from main-chain folding angles J. Mol. Biol. 219, 481-497 (1991) |
| OVEJ920101 |
STR matrix from structure-based alignments (Overington et al., 1992)
LIT:1811128 PMID:1304904 Overington, J., Donnelly, D., Johnson, M.S., Sali, A. and Blundell, T.L. Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds Protein Science 1, 216-226 (1992) |
| QU_C930101 |
Cross-correlation coefficients of preference factors
main chain (Qu et al., 1993)
LIT:1906100 PMID:8381879 Qu, C., Lai, L., Xu, X. and Tang, Y. Phyletic relationships of protein structures based on spatial prefernce of residues J. Mol. Evol. 36, 67-78 (1993) |
| QU_C930102 |
Cross-correlation coefficients of preference factors
side chain (Qu et al., 1993)
LIT:1906100 PMID:8381879 Qu, C., Lai, L., Xu, X. and Tang, Y. Phyletic relationships of protein structures based on spatial prefernce of residues J. Mol. Evol. 36, 67-78 (1993) |
| QU_C930103 |
The mutant distance based on spatial preference factor (Qu et al., 1993)
LIT:1906100 PMID:8381879 Qu, C., Lai, L., Xu, X. and Tang, Y. Phyletic relationships of protein structures based on spatial prefernce of residues J. Mol. Evol. 36, 67-78 (1993) |
| RISJ880101 |
Scoring matrix (Risler et al., 1988)
LIT:1505154 PMID:3221397 Risler, J.L., Delorme, M.O., Delacroix, H. and Henaut, A. Amino acid substitutions in structurally related proteins A pattern recognition approach Determination of a new and efficient scoring matrix J. Mol. Biol. 204, 1019-1029 (1988) |
| TUDE900101 |
isomorphicity of replacements (Tudos et al., 1990)
LIT:1616619 PMID:2279846 Tudos, E., Cserzo, M. and Simon, I. Predicting isomorphic residue replacements for protein design Int. J. Peptide Protein Res. 36, 236-239 (1990) * Diagonal elements are missing. * We use 100 as diagonal elements. |
| AZAE970101 |
The single residue substitution matrix from interchanges of
spatially neighbouring residues (Azarya-Sprinzak et al., 1997)
PMID:9488136 Azarya-Sprinzak, E., Naor, D., Wolfson, H.J. and Nussinov, R. Interchanges of spatially neighbouring residues in structurally conserved environments. Protein Engineering 10, 1109-1122 (1997) |
| AZAE970102 |
The substitution matrix derived from spatially conserved motifs
(Azarya-Sprinzak et al., 1997)
PMID:9488136 Azarya-Sprinzak, E., Naor, D., Wolfson, H.J. and Nussinov, R. Interchanges of spatially neighbouring residues in structurally conserved environments. Protein Engineering 10, 1109-1122 (1997) |
| RIER950101 |
Hydrophobicity scoring matrix (Riek et al., 1995)
PMID:7715195 Riek, R.P., Handschumacher, M.D., Sung, S.S., Tan, M., Glynias, M.J., Schluchter, M.D., Novotny, J. and Graham, R.M. Evolutionary conservation of both the hydrophilic and hydrophobic nature of transmembrane residues. J. Theor. Biol. 172, 245-258 (1995) |
| WEIL970101 |
WAC matrix constructed from amino acid comparative profiles (Wei et al., 1997)
PMID:9390315 Wei, L., Altman, R.B. and Chang, J.T. Using the radial distributions of physical features to compare amino acid environments and align amino acid sequences. Pac. Symp. Biocomput. 1997 5, 465-476 (1997) |
| WEIL970102 |
Difference matrix obtained by subtracting the BLOSUM62 from the WAC
matrix (Wei et al., 1997)
PMID:9390315 Wei, L., Altman, R.B. and Chang, J.T. Using the radial distributions of physical features to compare amino acid environments and align amino acid sequences. Pac. Symp. Biocomput. 1997 5, 465-476 (1997) |
| MEHP950101 |
(Mehta et al., 1995)
LIT:2213135 PMID:8580842 Mehta, P.K., Heringa, J. and Argos, P. A simple and fast approach to prediction of protein secondary structure from multiply aligned sequences with accuracy above 70% Protein Science 4, 2517-2525 (1995) |
| MEHP950102 |
(Mehta et al., 1995)
LIT:2213135 PMID:8580842 Mehta, P.K., Heringa, J. and Argos, P. A simple and fast approach to prediction of protein secondary structure from multiply aligned sequences with accuracy above 70% Protein Science 4, 2517-2525 (1995) |
| MEHP950103 |
(Mehta et al., 1995)
LIT:2213135 PMID:8580842 Mehta, P.K., Heringa, J. and Argos, P. A simple and fast approach to prediction of protein secondary structure from multiply aligned sequences with accuracy above 70% Protein Science 4, 2517-2525 (1995) |
| KAPO950101 |
(Kapp et al., 1995)
LIT:2124159 PMID:8535255 Kapp, O.H., Moens, L., Vanfleteren, J., Trotman, C.N., Suzuki, T. and Vinogradov, S.N. Alignment of 700 globin sequences: extent of amino acid substitution and its correlation with variation in volume Protein Science 4, 2179-2190 (1995) |
| VOGG950101 |
(Vogt et al., 1995)
LIT:2114150 PMID:7602593 Vogt G, Etzold T, Argos P An assessment of amino acid exchange matrices in aligning protein sequences: the twilight zone revisited J. Mol. Biol. 249, 816-831 (1995) |
| KOSJ950101 |
Context-dependent optimal substitution matrices for exposed helix
(Koshi-Goldstein, 1995)
LIT:2124140 PMID:8577693 Koshi, J.M. and Goldstein, R.A. Context-dependent optimal substitution matrices. Protein Engineering 8, 641-645 (1995) |
| KOSJ950102 |
Context-dependent optimal substitution matrices for exposed beta
(Koshi-Goldstein, 1995)
LIT:2124140 PMID:8577693 Koshi, J.M. and Goldstein, R.A. Context-dependent optimal substitution matrices. Protein Engineering 8, 641-645 (1995) |
| KOSJ950103 |
Context-dependent optimal substitution matrices for exposed turn
(Koshi-Goldstein, 1995)
LIT:2124140 PMID:8577693 Koshi, J.M. and Goldstein, R.A. Context-dependent optimal substitution matrices. Protein Engineering 8, 641-645 (1995) |
| KOSJ950104 |
Context-dependent optimal substitution matrices for exposed coil
(Koshi-Goldstein, 1995)
LIT:2124140 PMID:8577693 Koshi, J.M. and Goldstein, R.A. Context-dependent optimal substitution matrices. Protein Engineering 8, 641-645 (1995) |
| KOSJ950105 |
Context-dependent optimal substitution matrices for buried helix
(Koshi-Goldstein, 1995)
LIT:2124140 PMID:8577693 Koshi, J.M. and Goldstein, R.A. Context-dependent optimal substitution matrices. Protein Engineering 8, 641-645 (1995) |
| KOSJ950106 |
Context-dependent optimal substitution matrices for buried beta
(Koshi-Goldstein, 1995)
LIT:2124140 PMID:8577693 Koshi, J.M. and Goldstein, R.A. Context-dependent optimal substitution matrices. Protein Engineering 8, 641-645 (1995) |
| KOSJ950107 |
Context-dependent optimal substitution matrices for buried turn
(Koshi-Goldstein, 1995)
LIT:2124140 PMID:8577693 Koshi, J.M. and Goldstein, R.A. Context-dependent optimal substitution matrices. Protein Engineering 8, 641-645 (1995) |
| KOSJ950108 |
Context-dependent optimal substitution matrices for buried coil
(Koshi-Goldstein, 1995)
LIT:2124140 PMID:8577693 Koshi, J.M. and Goldstein, R.A. Context-dependent optimal substitution matrices. Protein Engineering 8, 641-645 (1995) |
| KOSJ950109 |
Context-dependent optimal substitution matrices for alpha helix
(Koshi-Goldstein, 1995)
LIT:2124140 PMID:8577693 Koshi, J.M. and Goldstein, R.A. Context-dependent optimal substitution matrices. Protein Engineering 8, 641-645 (1995) |
| KOSJ950110 |
Context-dependent optimal substitution matrices for beta sheet
(Koshi-Goldstein, 1995)
LIT:2124140 PMID:8577693 Koshi, J.M. and Goldstein, R.A. Context-dependent optimal substitution matrices. Protein Engineering 8, 641-645 (1995) |
| KOSJ950111 |
Context-dependent optimal substitution matrices for turn
(Koshi-Goldstein, 1995)
LIT:2124140 PMID:8577693 Koshi, J.M. and Goldstein, R.A. Context-dependent optimal substitution matrices. Protein Engineering 8, 641-645 (1995) |
| KOSJ950112 |
Context-dependent optimal substitution matrices for coil
(Koshi-Goldstein, 1995)
LIT:2124140 PMID:8577693 Koshi, J.M. and Goldstein, R.A. Context-dependent optimal substitution matrices. Protein Engineering 8, 641-645 (1995) |
| KOSJ950113 |
Context-dependent optimal substitution matrices for exposed residues
(Koshi-Goldstein, 1995)
LIT:2124140 PMID:8577693 Koshi, J.M. and Goldstein, R.A. Context-dependent optimal substitution matrices. Protein Engineering 8, 641-645 (1995) |
| KOSJ950114 |
Context-dependent optimal substitution matrices for buried residues
(Koshi-Goldstein, 1995)
LIT:2124140 PMID:8577693 Koshi, J.M. and Goldstein, R.A. Context-dependent optimal substitution matrices. Protein Engineering 8, 641-645 (1995) |
| KOSJ950115 |
Context-dependent optimal substitution matrices for all residues
(Koshi-Goldstein, 1995)
LIT:2124140 PMID:8577693 Koshi, J.M. and Goldstein, R.A. Context-dependent optimal substitution matrices. Protein Engineering 8, 641-645 (1995) |
| OVEJ920102 |
Environment-specific amino acid substitution matrix for alpha residues
(Overington et al., 1992)
LIT:1811128 PMID:1304904 Overington, J., Donnelly, D., Johnson, M.S., Sali, A. and Blundell, T.L. Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds Protein Science 1, 216-226 (1992) |
| OVEJ920103 |
Environment-specific amino acid substitution matrix for beta residues
(Overington et al., 1992)
LIT:1811128 PMID:1304904 Overington, J., Donnelly, D., Johnson, M.S., Sali, A. and Blundell, T.L. Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds Protein Science 1, 216-226 (1992) |
| OVEJ920104 |
Environment-specific amino acid substitution matrix for accessible
residues (Overington et al., 1992)
LIT:1811128 PMID:1304904 Overington, J., Donnelly, D., Johnson, M.S., Sali, A. and Blundell, T.L. Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds Protein Science 1, 216-226 (1992) |
| OVEJ920105 |
Environment-specific amino acid substitution matrix for inaccessible residues
(Overington et al., 1992)
LIT:1811128 PMID:1304904 Overington, J., Donnelly, D., Johnson, M.S., Sali, A. and Blundell, T.L. Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds Protein Science 1, 216-226 (1992) |
| LINK010101 |
Substitution matrices from an neural network model (Lin et al., 2001)
PMID:11694178 Lin, K., May, A.C. and Taylor, W.R. Amino acid substitution matrices from an artificial neural network model J Comput Biol. 8, 471-481 (2001) |
| BLAJ010101 |
Matrix built from structural superposition data for identifying potential
remote homologues (Blake-Cohen, 2001)
PMID:11254392 Blake, J.D. and Cohen, F.E. Pairwise sequence alignment below the twilight zone J Mol Biol. 307, 721-735 (2001) |
| PRLA000101 |
Structure derived matrix (SDM) for alignment of distantly related sequences
(Prlic et al., 2000)
PMID:10964983 Prlic, A., Domingues, F.S. and Sippl, M.J. Structure-derived substitution matrices for alignment of distantly related sequences Protein Eng. 13, 545-550 (2000) |
| PRLA000102 |
Homologous structure dereived matrix (HSDM) for alignment of distantly
related sequences (Prlic et al., 2000)
PMID:10964983 Prlic, A., Domingues, F.S. and Sippl, M.J. Structure-derived substitution matrices for alignment of distantly related sequences Protein Eng. 13, 545-550 (2000) |
| DOSZ010101 |
Amino acid similarity matrix based on the sausage force
field (Dosztanyi-Torda, 2001)
PMID:11524370 Dosztanyi, Z. and Torda, A.E. Amino acid similarity matrices based on force fields Bioinformatics. 17, 686-699 (2001) * #SM_SAUSAGE * #Amino acid similarity matrix based on the sausage force field * #Supplementary material * #http://www.rsc.anu.edu.au/~zsuzsa/suppl/matrices/SM_SAUSAGE * #Zsuzsanna Doszt?yi and Andrew E. Torda * #Amino acid similarity matrices based on force fields * #The amino acids are ordered according to the first principal component of the SM_SAUSAGE matrix. * #The native cysteine residues were devided into two subsets depending on their covalent state. * #Three rows correspond to cysteines: disulfide bonded (O), free cysteines (J) and all cysteines (C). |
| DOSZ010102 |
Normalised version of SM_SAUSAGE (Dosztanyi-Torda, 2001)
PMID:11524370 Dosztanyi, Z. and Torda, A.E. Amino acid similarity matrices based on force fields Bioinformatics. 17, 686-699 (2001) * #SM_SAUS_NORM * #Normalised version of SM_SAUSAGE * #For each matrix element of SM_SAUSAGE, the average over its column and row were subtracted. * #Supplementary material * #http://www.rsc.anu.edu.au/~zsuzsa/suppl/matrices/SM_SAUS_NORM * #Zsuzsanna Doszt?yi and Andrew E. Torda * #Amino acid similarity matrices based on force fields * #The amino acids are ordered according to the first principal component of the SM_SAUSAGE matrix. |
| DOSZ010103 |
An amino acid similarity matrix based on the THREADER force field
(Dosztanyi-Torda, 2001)
PMID:11524370 Dosztanyi, Z. and Torda, A.E. Amino acid similarity matrices based on force fields Bioinformatics. 17, 686-699 (2001) * #SM_THREADER * #An amino acid similarity matrix based on the THREADER force field (Jones, DT et al.Nature, 358,86-89). * #Supplementary material * #http://www.rsc.anu.edu.au/~zsuzsa/suppl/matrices/SM_THREADER * #Zsuzsanna Doszt?yi and Andrew E. Torda * #Amino acid similarity matrices based on force fields * #The amino acids are ordered according to the first principal component of the SM_SAUSAGE matrix. |
| DOSZ010104 |
Normalised version of SM_THREADER (Dosztanyi-Torda, 2001)
PMID:11524370 Dosztanyi, Z. and Torda, A.E. Amino acid similarity matrices based on force fields Bioinformatics. 17, 686-699 (2001) * #SM_THREAD_NORM * #Normalised version of SM_THREADER * #based on the THREADER force field (Jones, DT et al.Nature, 358,86-89) * #For each matrix element of SM_THREADER, the average over its column and row were subtracted. * #Supplementary material * #http://www.rsc.anu.edu.au/~zsuzsa/suppl/matrices/SM_THREAD_NORM * #Zsuzsanna Doszt?yi and Andrew E. Torda * #Amino acid similarity matrices based on force fields * #The amino acids are ordered according to the first principal component of the SM_SAUSAGE matrix. |
| GIAG010101 |
Residue substitutions matrix from thermo/mesophilic to psychrophilic
enzymes (Gianese et al., 2001)
PMID:11342709 Gianese, G., Argos, P. and Pascarella, S. Structural adaptation of enzymes to low temperatures Protein Eng. 14, 141-148 (2001) * (rows = WARM, cols = COLD) |
| DAYM780302 |
Log odds matrix for 40 PAMs (Dayhoff et al., 1978)
R
Dayhoff, M.O., Schwartz, R.M. and Orcutt, B.C. A model of evolutionary change in proteins In "Atlas of Protein Sequence and Structure", Vol.5, Suppl.3 (Dayhoff, M.O., ed.), National Biomedical Research Foundation, Washington, D.C., p.352 (1978) * # * # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] * # * # PAM 40 substitution matrix, scale = ln(2)/2 = 0.346574 * # * # Expected score = -4.27, Entropy = 2.26 bits * # * # Lowest score = -15, Highest score = 13 * # |
| HENS920104 |
BLOSUM50 substitution matrix (Henikoff-Henikoff, 1992)
LIT:1902106 PMID:1438297 Henikoff, S. and Henikoff, J.G. Amino acid substitution matrices from protein blocks Proc. Natl. Acad. Sci. USA 89, 10915-10919 (1992) * # Matrix made by matblas from blosum50.iij * # BLOSUM Clustered Scoring Matrix in 1/3 Bit Units * # Blocks Database = /data/blocks_5.0/blocks.dat * # Cluster Percentage: >= 50 * # Entropy = 0.4808, Expected = -0.3573 |
| QUIB020101 |
STROMA score matrix for the alignment of known distant homologs
(Qian-Goldstein, 2002)
PMID:12211027 Qian, B. and Goldstein, R.A. Optimization of a new score function for the generation of accurate alignments Proteins. 48, 605-610 (2002) |
| VT160 | T. Miller and M. Vingron Modeling Amino Acid Replacement Journal of Computational Biology, 7(6):761-776, 2000. Abstract: The estimation of amino acid replacement frequencies during molecular evolution is crucial for many applications in sequence analysis. Score matrices for database search programs or phylogenetic analysis rely on such models of protein evolution. Pioneering work was done by M. Dayhoff et al. (Atlas of Protein Sequences and Structure, 1978, 5, 345-352), who formulated a Markov model of evolution and derived the famous PAM score matrices. Her estimation procedure for amino acid exchange frequencies is restricted to pairs of proteins that have a constant and small degree of divergence. Here we present an improved estimator, called the resolvent method, that is not subject to these limitations. This extension of Dayhoff's approach enables us to estimate an amino acid substitution model from alignments of varying degree of divergence. Extensive simulations show the capability of the new estimator to recover accurately the exchange frequencies among amino acids. Based on the SYSTERS database of aligned protein families (Krause & Vingron, Bioinformatics, 1998, 14(5), 430-438) we recompute a series of score matrices. |