Difference between revisions of "PsiBlast in Big80 (PKU)"
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| − | We performed a PsiBlast search with 5 iterations and standard settings in the big_80 database. We choose this database to include more distant homologs and have highly similar sequences excluded from the beginning. Below we present the PSSM of PAH of the [[Predicting_the_Effect_of_SNPs_(PKU)#Our dataset|SNP-sites]], gained from the '''-Q''' parameter of PsiBlast. Highly conserved (i.e. the score and observed frequency are highest for the match) positions are 76E, 243R, 322A and 408R, unstable (i.e. there is a substitution with higher score or frequency) are 87S, 172Q, 255L, 276M and 337G. At 87S, 158R, 172Q and 276M the score or frequency of the SNP is equal or higher than the score |
+ | We performed a PsiBlast search with 5 iterations and standard settings in the big_80 database. We choose this database to include more distant homologs and have highly similar sequences excluded from the beginning. Below we present the PSSM of PAH of the [[Predicting_the_Effect_of_SNPs_(PKU)#Our dataset|SNP-sites]], gained from the '''-Q''' parameter of PsiBlast, the SNPs are marked as '''bold''' letters. Highly conserved (i.e. the score and observed frequency are highest for the match) positions are 76E, 243R, 322A and 408R, unstable (i.e. there is a substitution with higher score or frequency) are 87S, 172Q, 255L, 276M and 337G. At 87S, 158R, 172Q and 276M the score or frequency of the SNP is equal or higher than the score or frequency of the unmutated residue.<br /> |
In summary, 76E, 243R, 322A and 408R appear conserved, 87S, 158R, 172Q, 255L, 276M and 337G appear likely to be mutated. |
In summary, 76E, 243R, 322A and 408R appear conserved, 87S, 158R, 172Q, 255L, 276M and 337G appear likely to be mutated. |
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Revision as of 21:40, 18 June 2012
We performed a PsiBlast search with 5 iterations and standard settings in the big_80 database. We choose this database to include more distant homologs and have highly similar sequences excluded from the beginning. Below we present the PSSM of PAH of the SNP-sites, gained from the -Q parameter of PsiBlast, the SNPs are marked as bold letters. Highly conserved (i.e. the score and observed frequency are highest for the match) positions are 76E, 243R, 322A and 408R, unstable (i.e. there is a substitution with higher score or frequency) are 87S, 172Q, 255L, 276M and 337G. At 87S, 158R, 172Q and 276M the score or frequency of the SNP is equal or higher than the score or frequency of the unmutated residue.
In summary, 76E, 243R, 322A and 408R appear conserved, 87S, 158R, 172Q, 255L, 276M and 337G appear likely to be mutated.
Last position-specific scoring matrix computed, weighted observed percentages rounded down, information per position, and relative weight of gapless real matches to pseudocounts
A R N D C Q E G H I L K M F P S T W Y V A R N D C Q E G H I L K M F P S T W Y V
76 E 0 0 1 2 -1 2 4 -2 1 -5 -4 0 -2 -5 -3 0 1 -6 -3 -3 8 6 6 9 1 9 30 3 3 0 1 5 1 0 1 6 8 0 1 2 0.48 inf
87 S -1 1 1 0 1 0 -1 -2 1 1 0 0 2 -1 0 -1 -1 4 0 0 5 8 6 5 3 5 4 3 3 8 9 5 5 3 4 5 4 5 3 7 0.08 inf
158 R 0 1 1 -1 -2 1 1 0 -1 -2 -2 1 1 1 1 1 1 -2 -1 -2 8 8 8 0 0 8 8 8 0 0 1 8 8 8 8 8 8 0 0 0 0.14 inf
172 Q 0 0 0 0 2 1 0 0 1 0 0 0 1 0 -2 0 0 -3 -1 0 6 6 6 6 6 6 6 6 6 6 6 6 6 6 0 6 6 0 0 6 0.03 inf
243 R 0 5 -3 -4 -1 0 -1 -3 -2 -1 -2 -1 -2 -3 -4 0 -1 -4 1 4 7 30 0 0 1 5 3 1 1 1 3 3 0 0 0 7 2 0 4 30 0.51 inf
255 L -3 -4 -4 -4 0 -4 -4 -4 -3 1 3 -4 3 6 -4 -3 -1 -2 2 -1 1 0 0 0 2 0 1 1 0 9 30 0 8 35 0 1 4 0 6 1 0.74 inf
276 M -2 0 1 4 -3 0 1 0 0 -2 0 0 0 0 -2 -1 -1 -3 -1 -1 1 3 7 31 0 1 12 6 2 0 10 6 4 4 1 3 1 0 2 6 0.24 inf
322 A 3 1 -2 -2 -2 1 -1 0 -2 -1 -2 0 0 -2 -1 2 0 -3 -2 -1 43 7 0 0 0 7 2 6 0 3 2 3 2 1 1 16 3 0 0 3 0.27 inf
337 G 0 -1 3 3 -3 1 0 0 1 -2 -2 0 -2 -4 2 -1 -1 -4 -3 -2 6 3 22 18 0 6 5 8 5 1 5 6 0 0 13 1 1 0 0 2 0.32 inf
408 R -1 5 -1 1 -4 0 -1 -3 0 -4 -1 4 -3 -4 -3 -2 -1 -4 -3 -3 4 42 2 7 0 2 2 1 3 0 7 23 0 0 0 1 4 0 0 1 0.74 inf
K Lambda
Standard Ungapped 0.1380 0.3205
Standard Gapped 0.0410 0.2670
PSI Ungapped 0.1490 0.3176
PSI Gapped 0.0456 0.2670
