Module xi_covutils.matrices.blosum_50
Background and joint amino acid substitution frequencies used to calculate BLOSUM50 matrix.
Frequencies taken from the NCBI C++ toolkit source code. https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/algo/blast/composition_adjustment/matrix_frequency_data.c
Expand source code
"""
Background and joint amino acid substitution frequencies used to calculate
BLOSUM50 matrix.
Frequencies taken from the NCBI C++ toolkit source code.
https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/algo/blast/composition_adjustment/matrix_frequency_data.c
"""
BLOSUM_50_BG = [
7.6539470498057649e-02, 5.3250385307217402e-02, 4.3637061980733187e-02,
5.1393635127596211e-02, 2.2316032400410832e-02, 3.4923218698747475e-02,
5.6445304260661695e-02, 7.3850907051359951e-02, 2.4711032253042223e-02,
6.4065361639403171e-02, 9.5587467619348249e-02, 5.7876000358301254e-02,
2.4385897213061735e-02, 4.8098159196680347e-02, 4.0885461298433984e-02,
5.9478937760864596e-02, 5.2921707787277797e-02, 1.3706552419028580e-02,
3.3493684732315711e-02, 7.2433722397458003e-02
]
BLOSUM_50_JOINT = [
[
1.9177376165900414e-02, 2.7240376714546557e-03, 2.4031492992281512e-03,
2.5950400141435646e-03, 1.5161141503466080e-03, 2.1916331677173605e-03,
3.4448278914639618e-03, 6.2251471153775524e-03, 1.2127849526349368e-03,
3.5067963781079273e-03, 4.8064175187919377e-03, 3.3118156445774184e-03,
1.5929928229676674e-03, 2.0111462534334831e-03, 2.2367690269707355e-03,
6.2077372467778114e-03, 3.9182728585714704e-03, 4.8631739510959277e-04,
1.5289255743243066e-03, 5.4421693501580945e-03
],
[
2.7240376714546557e-03, 1.5249518561669190e-02, 1.9839339217171100e-03,
1.8569646551144466e-03, 5.0841145558634812e-04, 2.5241992415035875e-03,
2.9346714600391238e-03, 2.0330929248566329e-03, 1.2916661377324677e-03,
1.4850904029213015e-03, 2.8200506536265085e-03, 6.3631786906688794e-03,
8.8044244163237157e-04, 1.1827555704613821e-03, 1.1291633722052721e-03,
2.5480707779992882e-03, 2.0755623893205866e-03, 3.8597740102525838e-04,
1.2968650803478032e-03, 1.9767324973351923e-03
],
[
2.4031492992281512e-03, 1.9839339217171100e-03, 1.0064274648985122e-02,
3.4938528463521034e-03, 5.8526580393535813e-04, 1.5772225567522585e-03,
2.2654955215314441e-03, 3.1227790949497000e-03, 1.5032392778514345e-03,
1.2604525924282989e-03, 1.7212395367610532e-03, 2.6781179272946298e-03,
6.5072987349609041e-04, 9.2077070726659231e-04, 1.0780835837505738e-03,
3.1777703084905646e-03, 2.5607235691682607e-03, 2.2470939491808472e-04,
9.0102455753719311e-04, 1.4642269583191670e-03
],
[
2.5950400141435646e-03, 1.8569646551144466e-03, 3.4938528463521034e-03,
1.6142284245400377e-02, 4.9055796014848500e-04, 1.7355972391605227e-03,
4.8092932462930728e-03, 2.8256049847966923e-03, 1.1224039610689225e-03,
1.2187267471037043e-03, 1.8320202151810498e-03, 2.6483031701007680e-03,
5.4518900860208049e-04, 8.3372775443144032e-04, 1.4911089792375384e-03,
2.8168184837142236e-03, 2.2443557004503045e-03, 2.1629521399451062e-04,
8.6838200454238037e-04, 1.6071086977600263e-03
],
[
1.5161141503466080e-03, 5.0841145558634812e-04, 5.8526580393535813e-04,
4.9055796014848500e-04, 9.0790816399874165e-03, 3.7509694198458956e-04,
5.7443167694834051e-04, 8.6416125741413223e-04, 2.8532822032727102e-04,
8.3949095461630769e-04, 1.3866946702884293e-03, 5.9394346268641564e-04,
3.7056882781629923e-04, 6.0643258121975913e-04, 3.6775301298071699e-04,
1.1014893301583900e-03, 9.6593119839638185e-04, 9.5473415415687051e-05,
4.0265275985100583e-04, 1.3071530803028910e-03
],
[
2.1916331677173605e-03, 2.5241992415035875e-03, 1.5772225567522585e-03,
1.7355972391605227e-03, 3.7509694198458956e-04, 5.7288780946700701e-03,
3.2946407159359019e-03, 1.6542835961738131e-03, 1.0434512306085959e-03,
1.1246276733803604e-03, 1.8792097500823605e-03, 2.8672107479796771e-03,
8.1749695236423632e-04, 7.0039848968711364e-04, 1.0716022846036992e-03,
2.2199500917807818e-03, 1.4976248429072652e-03, 3.4211307677156259e-04,
8.6801232355735846e-04, 1.4099696811263587e-03
],
[
3.4448278914639618e-03, 2.9346714600391238e-03, 2.2654955215314441e-03,
4.8092932462930728e-03, 5.7443167694834051e-04, 3.2946407159359019e-03,
1.4137738860962050e-02, 2.2506310350989874e-03, 1.2713631289270268e-03,
1.5027392767795753e-03, 2.5813459827982222e-03, 4.3484287857007489e-03,
8.3289745544177065e-04, 1.2381529956170115e-03, 1.9357892959573676e-03,
2.9614835299989701e-03, 2.4465955340418752e-03, 4.2400226067181517e-04,
1.2320532047293646e-03, 1.9587224017250621e-03
],
[
6.2251471153775524e-03, 2.0330929248566329e-03, 3.1227790949497000e-03,
2.8256049847966923e-03, 8.6416125741413223e-04, 1.6542835961738131e-03,
2.2506310350989874e-03, 3.1590334199549770e-02, 1.0972793065146165e-03,
1.7523277816042203e-03, 2.6606416500206632e-03, 2.7990435215878512e-03,
9.3546770862675606e-04, 1.4703871152100261e-03, 1.8725532583338258e-03,
4.3892726706643180e-03, 2.4867404596474229e-03, 5.1106914401047939e-04,
1.1558215242534139e-03, 2.1542687026690753e-03
],
[
1.2127849526349368e-03, 1.2916661377324677e-03, 1.5032392778514345e-03,
1.1224039610689225e-03, 2.8532822032727102e-04, 1.0434512306085959e-03,
1.2713631289270268e-03, 1.0972793065146165e-03, 6.3804882118271523e-03,
6.5152626785360663e-04, 1.2931025418026663e-03, 1.3522962310675180e-03,
4.5805146362189403e-04, 8.9702000483341665e-04, 5.8791282749163360e-04,
1.2089586814863836e-03, 8.5349236685497410e-04, 1.6088475111162087e-04,
1.2994388028749182e-03, 7.4034388655116329e-04
],
[
3.5067963781079273e-03, 1.4850904029213015e-03, 1.2604525924282989e-03,
1.2187267471037043e-03, 8.3949095461630769e-04, 1.1246276733803604e-03,
1.5027392767795753e-03, 1.7523277816042203e-03, 6.5152626785360663e-04,
1.3999757001274281e-02, 1.0390816757632199e-02, 1.7363767070665819e-03,
2.2467399442463766e-03, 3.0498186875911964e-03, 1.3390359572833434e-03,
2.0791955470136677e-03, 2.9182353019045755e-03, 4.5881135439627285e-04,
1.7726237165460320e-03, 1.0732172589653342e-02
],
[
4.8064175187919377e-03, 2.8200506536265085e-03, 1.7212395367610532e-03,
1.8320202151810498e-03, 1.3866946702884293e-03, 1.8792097500823605e-03,
2.5813459827982222e-03, 2.6606416500206632e-03, 1.2931025418026663e-03,
1.0390816757632199e-02, 3.0409269773873687e-02, 2.6510115013545226e-03,
4.1722701893507309e-03, 5.8008510370760203e-03, 1.7339408813938210e-03,
2.9030148705129709e-03, 3.8403853123581615e-03, 7.8809411669902049e-04,
2.7481481703784771e-03, 9.1689424893657400e-03
],
[
3.3118156445774184e-03, 6.3631786906688794e-03, 2.6781179272946298e-03,
2.6483031701007680e-03, 5.9394346268641564e-04, 2.8672107479796771e-03,
4.3484287857007489e-03, 2.7990435215878512e-03, 1.3522962310675180e-03,
1.7363767070665819e-03, 2.6510115013545226e-03, 1.2999587798271149e-02,
9.6710745846319019e-04, 1.2387025901401758e-03, 1.8070838729286381e-03,
3.0739875836290694e-03, 2.5875240617244397e-03, 3.6617320485888769e-04,
1.2944286682925433e-03, 2.1916787299081464e-03
],
[
1.5929928229676674e-03, 8.8044244163237157e-04, 6.5072987349609041e-04,
5.4518900860208049e-04, 3.7056882781629923e-04, 8.1749695236423632e-04,
8.3289745544177065e-04, 9.3546770862675606e-04, 4.5805146362189403e-04,
2.2467399442463766e-03, 4.1722701893507309e-03, 9.6710745846319019e-04,
2.8637130884961001e-03, 1.2334264856852042e-03, 5.4319510273222540e-04,
9.8962843407290630e-04, 1.1386579188117374e-03, 2.5453642381012927e-04,
7.4966082446689317e-04, 2.1431247883570799e-03
],
[
2.0111462534334831e-03, 1.1827555704613821e-03, 9.2077070726659231e-04,
8.3372775443144032e-04, 6.0643258121975913e-04, 7.0039848968711364e-04,
1.2381529956170115e-03, 1.4703871152100261e-03, 8.9702000483341665e-04,
3.0498186875911964e-03, 5.8008510370760203e-03, 1.2387025901401758e-03,
1.2334264856852042e-03, 1.5352527520022995e-02, 7.3889079577318679e-04,
1.5819841076161790e-03, 1.4517880681388670e-03, 8.8872966327839206e-04,
3.9057132596179516e-03, 2.9949355095799514e-03
],
[
2.2367690269707355e-03, 1.1291633722052721e-03, 1.0780835837505738e-03,
1.4911089792375384e-03, 3.6775301298071699e-04, 1.0716022846036992e-03,
1.9357892959573676e-03, 1.8725532583338258e-03, 5.8791282749163360e-04,
1.3390359572833434e-03, 1.7339408813938210e-03, 1.8070838729286381e-03,
5.4319510273222540e-04, 7.3889079577318679e-04, 1.7056411057608904e-02,
1.8468214541146135e-03, 1.6196921560667427e-03, 2.3541955953234630e-04,
6.4111850267928403e-04, 1.5531163167895289e-03
],
[
6.2077372467778114e-03, 2.5480707779992882e-03, 3.1777703084905646e-03,
2.8168184837142236e-03, 1.1014893301583900e-03, 2.2199500917807818e-03,
2.9614835299989701e-03, 4.3892726706643180e-03, 1.2089586814863836e-03,
2.0791955470136677e-03, 2.9030148705129709e-03, 3.0739875836290694e-03,
9.8962843407290630e-04, 1.5819841076161790e-03, 1.8468214541146135e-03,
1.1119087492164673e-02, 4.7130010640939217e-03, 3.1984588103465904e-04,
1.2969411223575139e-03, 2.9238790831836834e-03
],
[
3.9182728585714704e-03, 2.0755623893205866e-03, 2.5607235691682607e-03,
2.2443557004503045e-03, 9.6593119839638185e-04, 1.4976248429072652e-03,
2.4465955340418752e-03, 2.4867404596474229e-03, 8.5349236685497410e-04,
2.9182353019045755e-03, 3.8403853123581615e-03, 2.5875240617244397e-03,
1.1386579188117374e-03, 1.4517880681388670e-03, 1.6196921560667427e-03,
4.7130010640939217e-03, 9.9511225720898735e-03, 3.6462369214353146e-04,
1.2243502023766173e-03, 4.0630285182107874e-03
],
[
4.8631739510959277e-04, 3.8597740102525838e-04, 2.2470939491808472e-04,
2.1629521399451062e-04, 9.5473415415687051e-05, 3.4211307677156259e-04,
4.2400226067181517e-04, 5.1106914401047939e-04, 1.6088475111162087e-04,
4.5881135439627285e-04, 7.8809411669902049e-04, 3.6617320485888769e-04,
2.5453642381012927e-04, 8.8872966327839206e-04, 2.3541955953234630e-04,
3.1984588103465904e-04, 3.6462369214353146e-04, 5.8917653327232667e-03,
8.1035438644761436e-04, 4.8135675107584730e-04
],
[
1.5289255743243066e-03, 1.2968650803478032e-03, 9.0102455753719311e-04,
8.6838200454238037e-04, 4.0265275985100583e-04, 8.6801232355735846e-04,
1.2320532047293646e-03, 1.1558215242534139e-03, 1.2994388028749182e-03,
1.7726237165460320e-03, 2.7481481703784771e-03, 1.2944286682925433e-03,
7.4966082446689317e-04, 3.9057132596179516e-03, 6.4111850267928403e-04,
1.2969411223575139e-03, 1.2243502023766173e-03, 8.1035438644761436e-04,
7.7325651605433090e-03, 1.7646048865917325e-03
],
[
5.4421693501580945e-03, 1.9767324973351923e-03, 1.4642269583191670e-03,
1.6071086977600263e-03, 1.3071530803028910e-03, 1.4099696811263587e-03,
1.9587224017250621e-03, 2.1542687026690753e-03, 7.4034388655116329e-04,
1.0732172589653342e-02, 9.1689424893657400e-03, 2.1916787299081464e-03,
2.1431247883570799e-03, 2.9949355095799514e-03, 1.5531163167895289e-03,
2.9238790831836834e-03, 4.0630285182107874e-03, 4.8135675107584730e-04,
1.7646048865917325e-03, 1.6356187478795130e-02
]
]