Module xi_covutils.matrices.blosum_62

Background and joint amino acid substitution frequencies used to calculate BLOSUM62 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
BLOSUM62 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_62_BG = [
  7.4216205067993410e-02, 5.1614486141284638e-02, 4.4645808512757915e-02,
  5.3626000838554413e-02, 2.4687457167944848e-02, 3.4259650591416023e-02,
  5.4311925684587502e-02, 7.4146941452644999e-02, 2.6212984805266227e-02,
  6.7917367618953756e-02, 9.8907868497150955e-02, 5.8155682303079680e-02,
  2.4990197579643110e-02, 4.7418459742284751e-02, 3.8538003320306206e-02,
  5.7229029476494421e-02, 5.0891364550287033e-02, 1.3029956129972148e-02,
  3.2281512313758580e-02, 7.2919098205619245e-02
]

BLOSUM_62_JOINT = [
  [
    2.1497573378347484e-02, 2.3470224274721213e-03, 1.9493235258876179e-03,
    2.1674844853066858e-03, 1.5903351423026848e-03, 1.9242657898716525e-03,
    2.9879059292799641e-03, 5.8158526388051033e-03, 1.1076584657559144e-03,
    3.1880644746334580e-03, 4.4186245468471547e-03, 3.3466571942021082e-03,
    1.3412107617355408e-03, 1.6360627863999076e-03, 2.1568959784943114e-03,
    6.2524987419815400e-03, 3.7180506975672363e-03, 4.0281679108936688e-04,
    1.2999956675626666e-03, 5.0679056444508912e-03
  ],
  [
    2.3470224274721213e-03, 1.7757465118386322e-02, 1.9786027128591904e-03,
    1.5865480081162602e-03, 3.9365984789376245e-04, 2.4858611089731411e-03,
    2.6933867548771758e-03, 1.7221140903704937e-03, 1.2407382229440791e-03,
    1.2435878276496955e-03, 2.4193952633248727e-03, 6.2339060289407083e-03,
    8.0309461712520876e-04, 9.3181986323789834e-04, 9.5783034332718700e-04,
    2.2660898636037261e-03, 1.7802796534180537e-03, 2.6571979312581875e-04,
    9.2634607111251918e-04, 1.5810185245264004e-03
  ],
  [
    1.9493235258876179e-03, 1.9786027128591904e-03, 1.4140291972553610e-02,
    3.7201973506001745e-03, 4.3845466068066216e-04, 1.5304436972610567e-03,
    2.2097156829738759e-03, 2.8591871815612977e-03, 1.4301072616183181e-03,
    9.9437221166923172e-04, 1.3690958423974782e-03, 2.4402105140841090e-03,
    5.2943633069226512e-04, 7.5004227978192801e-04, 8.6016459857770028e-04,
    3.1466019144814608e-03, 2.2360795375444384e-03, 1.6159545671597605e-04,
    7.0048422794024819e-04, 1.2014015528772706e-03
  ],
  [
    2.1674844853066858e-03, 1.5865480081162602e-03, 3.7201973506001745e-03,
    2.1274574617480089e-02, 3.9909227141697264e-04, 1.6481246723433428e-03,
    4.9158017471929655e-03, 2.5221102126636373e-03, 9.5384849402143984e-04,
    1.2347404942429857e-03, 1.5202051791453383e-03, 2.4453087721980561e-03,
    4.6429229320514104e-04, 7.6023722413111566e-04, 1.2373315413524663e-03,
    2.8035127901697272e-03, 1.8961512776990257e-03, 1.6218020183662784e-04,
    5.9842263937853702e-04, 1.3158365660538270e-03
  ],
  [
    1.5903351423026848e-03, 3.9365984789376245e-04, 4.3845466068066216e-04,
    3.9909227141697264e-04, 1.1931352277704348e-02, 3.0937204045913537e-04,
    3.8338775043186374e-04, 7.6951976030099293e-04, 2.2976387481074697e-04,
    1.0956590131781735e-03, 1.5682982157153873e-03, 5.0124929379033781e-04,
    3.7717165634097634e-04, 5.1389991547056834e-04, 3.6111795849154795e-04,
    1.0432626586831986e-03, 9.3041313726939057e-04, 1.4474923964368156e-04,
    3.4603772624580643e-04, 1.3606607271146112e-03
  ],
  [
    1.9242657898716525e-03, 2.4858611089731411e-03, 1.5304436972610567e-03,
    1.6481246723433428e-03, 3.0937204045913537e-04, 7.3292255467189687e-03,
    3.5385780499965817e-03, 1.3683038039160171e-03, 1.0489026828741754e-03,
    8.9102936026571569e-04, 1.6174411456311808e-03, 3.0968229715707327e-03,
    7.3993258722701268e-04, 5.4255147972143906e-04, 8.4668181752066874e-04,
    1.8931125300036275e-03, 1.3796838284921874e-03, 2.2737931366728891e-04,
    6.7584155312457842e-04, 1.1660966117775285e-03
  ],
  [
    2.9879059292799641e-03, 2.6933867548771758e-03, 2.2097156829738759e-03,
    4.9158017471929655e-03, 3.8338775043186374e-04, 3.5385780499965817e-03,
    1.6133927472163669e-02, 1.9380952488713059e-03, 1.3667885452189439e-03,
    1.2192061706431622e-03, 2.0030316026648431e-03, 4.1322603720305197e-03,
    6.7909745467514783e-04, 8.5179405867513139e-04, 1.4216207127018586e-03,
    2.9539180653600089e-03, 2.0493063257644955e-03, 2.6488552587183780e-04,
    8.7044186256788659e-04, 1.6987763526262680e-03
  ],
  [
    5.8158526388051033e-03, 1.7221140903704937e-03, 2.8591871815612977e-03,
    2.5221102126636373e-03, 7.6951976030099293e-04, 1.3683038039160171e-03,
    1.9380952488713059e-03, 3.7804346453413303e-02, 9.5813607255887238e-04,
    1.3849118546156933e-03, 2.0864716056392773e-03, 2.5392537741810947e-03,
    7.3281559749652399e-04, 1.1976708695723554e-03, 1.3641171883713547e-03,
    3.8342830901664762e-03, 2.1858459940987062e-03, 4.0740829083805248e-04,
    8.3467413018106177e-04, 1.8218235950233687e-03
  ],
  [
    1.1076584657559144e-03, 1.2407382229440791e-03, 1.4301072616183181e-03,
    9.5384849402143984e-04, 2.2976387481074697e-04, 1.0489026828741754e-03,
    1.3667885452189439e-03, 9.5813607255887238e-04, 9.2802502369336622e-03,
    5.8089627083019206e-04, 9.8696608463236094e-04, 1.1873625842258938e-03,
    3.8264639620910225e-04, 8.1041076335565583e-04, 4.7770135861914477e-04,
    1.1052034635193162e-03, 7.4371746073077327e-04, 1.5168037757411286e-04,
    1.5213771111755425e-03, 6.4882907765797669e-04
  ],
  [
    3.1880644746334580e-03, 1.2435878276496955e-03, 9.9437221166923172e-04,
    1.2347404942429857e-03, 1.0956590131781735e-03, 8.9102936026571569e-04,
    1.2192061706431622e-03, 1.3849118546156933e-03, 5.8089627083019206e-04,
    1.8441526588740136e-02, 1.1382470627796603e-02, 1.5655862274689192e-03,
    2.5081290988482057e-03, 3.0458868657559346e-03, 1.0068164685944146e-03,
    1.7225081689171561e-03, 2.6953622613315018e-03, 3.6183761166072852e-04,
    1.3821121844492116e-03, 1.1972663837662637e-02
  ],
  [
    4.4186245468471547e-03, 2.4193952633248727e-03, 1.3690958423974782e-03,
    1.5202051791453383e-03, 1.5682982157153873e-03, 1.6174411456311808e-03,
    2.0030316026648431e-03, 2.0864716056392773e-03, 9.8696608463236094e-04,
    1.1382470627796603e-02, 3.7141460156350926e-02, 2.4634345023228079e-03,
    4.9293545515183088e-03, 5.4151301166464015e-03, 1.4146090399381900e-03,
    2.4277107072013821e-03, 3.3238031308707055e-03, 7.3206640617832933e-04,
    2.2096734692836624e-03, 9.4786263030457313e-03
  ],
  [
    3.3466571942021082e-03, 6.2339060289407083e-03, 2.4402105140841090e-03,
    2.4453087721980561e-03, 5.0124929379033781e-04, 3.0968229715707327e-03,
    4.1322603720305197e-03, 2.5392537741810947e-03, 1.1873625842258938e-03,
    1.5655862274689192e-03, 2.4634345023228079e-03, 1.6113385590544604e-02,
    9.0876633395557617e-04, 9.4875149773685364e-04, 1.5773020912564391e-03,
    3.1016069999481111e-03, 2.3467014804084987e-03, 2.7198500003555514e-04,
    9.9908866586876396e-04, 1.9360424083099779e-03
  ],
  [
    1.3412107617355408e-03, 8.0309461712520876e-04, 5.2943633069226512e-04,
    4.6429229320514104e-04, 3.7717165634097634e-04, 7.3993258722701268e-04,
    6.7909745467514783e-04, 7.3281559749652399e-04, 3.8264639620910225e-04,
    2.5081290988482057e-03, 4.9293545515183088e-03, 9.0876633395557617e-04,
    4.0477309321969848e-03, 1.1901770463553603e-03, 4.0824445213456919e-04,
    8.5603787638552766e-04, 1.0095451907679563e-03, 1.9872537223131380e-04,
    5.7145288352831449e-04, 2.3123361470140736e-03
  ],
  [
    1.6360627863999076e-03, 9.3181986323789834e-04, 7.5004227978192801e-04,
    7.6023722413111566e-04, 5.1389991547056834e-04, 5.4255147972143906e-04,
    8.5179405867513139e-04, 1.1976708695723554e-03, 8.1041076335565583e-04,
    3.0458868657559346e-03, 5.4151301166464015e-03, 9.4875149773685364e-04,
    1.1901770463553603e-03, 1.8277684015431908e-02, 5.2528021756783813e-04,
    1.1939618185901600e-03, 1.1624184369750680e-03, 8.4917468952377874e-04,
    4.2392005745634370e-03, 2.5763052227920180e-03
  ],
  [
    2.1568959784943114e-03, 9.5783034332718700e-04, 8.6016459857770028e-04,
    1.2373315413524663e-03, 3.6111795849154795e-04, 8.4668181752066874e-04,
    1.4216207127018586e-03, 1.3641171883713547e-03, 4.7770135861914477e-04,
    1.0068164685944146e-03, 1.4146090399381900e-03, 1.5773020912564391e-03,
    4.0824445213456919e-04, 5.2528021756783813e-04, 1.9066033679132538e-02,
    1.6662567934883051e-03, 1.3511005665728870e-03, 1.4152209821874487e-04,
    4.5224391125285910e-04, 1.2451325046931832e-03
  ],
  [
    6.2524987419815400e-03, 2.2660898636037261e-03, 3.1466019144814608e-03,
    2.8035127901697272e-03, 1.0432626586831986e-03, 1.8931125300036275e-03,
    2.9539180653600089e-03, 3.8342830901664762e-03, 1.1052034635193162e-03,
    1.7225081689171561e-03, 2.4277107072013821e-03, 3.1016069999481111e-03,
    8.5603787638552766e-04, 1.1939618185901600e-03, 1.6662567934883051e-03,
    1.2585947097159817e-02, 4.7004857686835334e-03, 2.8731729176487776e-04,
    1.0299846310599138e-03, 2.3587292053265561e-03
  ],
  [
    3.7180506975672363e-03, 1.7802796534180537e-03, 2.2360795375444384e-03,
    1.8961512776990257e-03, 9.3041313726939057e-04, 1.3796838284921874e-03,
    2.0493063257644955e-03, 2.1858459940987062e-03, 7.4371746073077327e-04,
    2.6953622613315018e-03, 3.3238031308707055e-03, 2.3467014804084987e-03,
    1.0095451907679563e-03, 1.1624184369750680e-03, 1.3511005665728870e-03,
    4.7004857686835334e-03, 1.2514818886617953e-02, 2.8575770858467209e-04,
    9.4161039895612720e-04, 3.6402328079338207e-03
  ],
  [
    4.0281679108936688e-04, 2.6571979312581875e-04, 1.6159545671597605e-04,
    1.6218020183662784e-04, 1.4474923964368156e-04, 2.2737931366728891e-04,
    2.6488552587183780e-04, 4.0740829083805248e-04, 1.5168037757411286e-04,
    3.6183761166072852e-04, 7.3206640617832933e-04, 2.7198500003555514e-04,
    1.9872537223131380e-04, 8.4917468952377874e-04, 1.4152209821874487e-04,
    2.8731729176487776e-04, 2.8575770858467209e-04, 6.4699301717154852e-03,
    8.8744160259272527e-04, 3.5578318710317554e-04
  ],
  [
    1.2999956675626666e-03, 9.2634607111251918e-04, 7.0048422794024819e-04,
    5.9842263937853702e-04, 3.4603772624580643e-04, 6.7584155312457842e-04,
    8.7044186256788659e-04, 8.3467413018106177e-04, 1.5213771111755425e-03,
    1.3821121844492116e-03, 2.2096734692836624e-03, 9.9908866586876396e-04,
    5.7145288352831449e-04, 4.2392005745634370e-03, 4.5224391125285910e-04,
    1.0299846310599138e-03, 9.4161039895612720e-04, 8.8744160259272527e-04,
    1.0246100213822419e-02, 1.5489827890922993e-03
  ],
  [
    5.0679056444508912e-03, 1.5810185245264004e-03, 1.2014015528772706e-03,
    1.3158365660538270e-03, 1.3606607271146112e-03, 1.1660966117775285e-03,
    1.6987763526262680e-03, 1.8218235950233687e-03, 6.4882907765797669e-04,
    1.1972663837662637e-02, 9.4786263030457313e-03, 1.9360424083099779e-03,
    2.3123361470140736e-03, 2.5763052227920180e-03, 1.2451325046931832e-03,
    2.3587292053265561e-03, 3.6402328079338207e-03, 3.5578318710317554e-04,
    1.5489827890922993e-03, 1.9631915140537640e-02
  ]
]