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.
FormatOutput 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 matrixSelect one of the standard pre-defined matrix.
Tail gapTail gap:
Alignment with tail gaps penalties
Alignment without tail gaps penalties
Gap Initiation penaltyGap Initiation penalty in average match units.
Gap Continuation penaltyGap Continuation penalty in average match units.
Match scoreMatch score, if Single-score scoring chosen (Similarity scoring only).
Mismatch penalty Mismatch penalty, if Single-score scoring chosen.
Score methodScoring 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.