Module xi_covutils.matrices.blosum_90

Background and joint amino acid substitution frequencies used to calculate BLOSUM90 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
BLOSUM90 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_90_BG = [
  7.2552570322773416e-02, 4.9204908670176822e-02, 4.1453803904895913e-02,
  5.4114599751069477e-02, 2.9605031943377283e-02, 3.3576453482421185e-02,
  5.5175092196696710e-02, 7.9252675455356913e-02, 2.4890326300616415e-02,
  6.6060229109246138e-02, 9.6973050911305106e-02, 5.3375686232455331e-02,
  2.4402790064347962e-02, 4.6515405498268582e-02, 3.8659721995628657e-02,
  5.8095437228457614e-02, 5.1596863495160232e-02, 1.5369491541399532e-02,
  3.5653734247116535e-02, 7.3472127649230390e-02
]

BLOSUM_90_JOINT = [
  [
    2.8941466476520718e-02, 1.8963172918503119e-03, 1.4296539454877236e-03,
    1.6120541525071418e-03, 1.4378045557717186e-03, 1.5518753295389346e-03,
    2.6715149842246304e-03, 4.9176944070822995e-03, 8.3429471034916194e-04,
    2.2806166994472367e-03, 3.1400426239163565e-03, 2.5717145234657262e-03,
    9.7190459199705012e-04, 1.1707482997247202e-03, 1.9972723941546994e-03,
    6.1234827650497045e-03, 3.4990592936902896e-03, 3.1628263576966828e-04,
    9.5781456962094815e-04, 4.2309560726043610e-03
  ],
  [
    1.8963172918503119e-03, 2.2892163644406403e-02, 1.4545259958564671e-03,
    1.1118856442462741e-03, 3.0043550945087249e-04, 2.0799816656266574e-03,
    1.9867845182036542e-03, 1.2814494483589008e-03, 1.0659803319010067e-03,
    8.7747376727426759e-04, 1.5563382766215293e-03, 5.6726070720652388e-03,
    5.5601248568691477e-04, 6.0014287440373390e-04, 7.7860213318230740e-04,
    1.7926007027022699e-03, 1.3337993839260983e-03, 1.8822355540425045e-04,
    6.3568077704304765e-04, 1.1439035919666126e-03
  ],
  [
    1.4296539454877236e-03, 1.4545259958564671e-03, 1.7753653137209658e-02,
    3.4122251157479486e-03, 3.5262434817793110e-04, 1.2595133876871906e-03,
    1.7189800468094042e-03, 2.1939494568804173e-03, 1.1268322842671913e-03,
    6.2771773800865524e-04, 9.0162895039764071e-04, 1.9751605656395136e-03,
    3.4437514139917542e-04, 4.5695294787233016e-04, 5.6210182826678802e-04,
    2.6415583911000790e-03, 1.8096241176560255e-03, 1.1361193219385239e-04,
    5.3166878528705414e-04, 7.8744578895086331e-04
  ],
  [
    1.6120541525071418e-03, 1.1118856442462741e-03, 3.4122251157479486e-03,
    2.8905985529761216e-02, 2.8205144393017687e-04, 1.2470706135571605e-03,
    4.8098591474193932e-03, 2.0787428065125128e-03, 7.3570523495442291e-04,
    6.1360733950558593e-04, 8.9746213145538078e-04, 1.7935339070485811e-03,
    2.8515554540729039e-04, 4.9706948686116547e-04, 8.3650620447870902e-04,
    2.1902661040309438e-03, 1.4770487412630099e-03, 9.6154148977656466e-05,
    4.1238640135342840e-04, 8.1983005205147035e-04
  ],
  [
    1.4378045557717186e-03, 3.0043550945087249e-04, 3.5262434817793110e-04,
    2.8205144393017687e-04, 1.8963924833314688e-02, 2.4062393656260663e-04,
    2.4018396300677406e-04, 5.1191591124580998e-04, 1.4262451141854431e-04,
    1.0187249201952210e-03, 1.2204913461061227e-03, 3.4081454298601579e-04,
    3.0855994042178013e-04, 5.4061743869703049e-04, 2.6341296370767072e-04,
    9.0081780182465609e-04, 8.3760722742725604e-04, 1.1402385673074935e-04,
    3.0875531409262481e-04, 1.2790175783090351e-03
  ],
  [
    1.5518753295389346e-03, 2.0799816656266574e-03, 1.2595133876871906e-03,
    1.2470706135571605e-03, 2.4062393656260663e-04, 1.1258473852655668e-02,
    3.3929068022966746e-03, 1.0135072388571143e-03, 1.0428112436817220e-03,
    6.2154432511249121e-04, 1.2200582014470405e-03, 2.6612615004061048e-03,
    6.9614541817054399e-04, 4.3847028249800182e-04, 6.3169039064483155e-04,
    1.5347331351459369e-03, 1.1633090191045159e-03, 1.8118969468635933e-04,
    4.8090269093961543e-04, 8.6038475380201306e-04
  ],
  [
    2.6715149842246304e-03, 1.9867845182036542e-03, 1.7189800468094042e-03,
    4.8098591474193932e-03, 2.4018396300677406e-04, 3.3929068022966746e-03,
    2.4082550387620767e-02, 1.5173914448105995e-03, 1.0609424122148584e-03,
    8.6556272233095357e-04, 1.2693446983220930e-03, 3.1728712431242272e-03,
    4.8675933771578960e-04, 5.2592632830518644e-04, 1.1283633992741310e-03,
    2.4358395159902540e-03, 1.7460695145653721e-03, 1.7186658965667723e-04,
    5.3762929629223334e-04, 1.3537458445130380e-03
  ],
  [
    4.9176944070822995e-03, 1.2814494483589008e-03, 2.1939494568804173e-03,
    2.0787428065125128e-03, 5.1191591124580998e-04, 1.0135072388571143e-03,
    1.5173914448105995e-03, 5.2105577140795424e-02, 6.6116372972342219e-04,
    7.9279793619671047e-04, 1.4084669216931525e-03, 1.8091800840455807e-03,
    4.5905141534639837e-04, 7.2640563736237702e-04, 9.1606958049118977e-04,
    3.2250721573096343e-03, 1.6376154647606311e-03, 2.8505580568873712e-04,
    5.3377971995623207e-04, 1.1777891482397749e-03
  ],
  [
    8.3429471034916194e-04, 1.0659803319010067e-03, 1.1268322842671913e-03,
    7.3570523495442291e-04, 1.4262451141854431e-04, 1.0428112436817220e-03,
    1.0609424122148584e-03, 6.6116372972342219e-04, 1.1500733945516558e-02,
    3.8185691425617459e-04, 6.9827301155994540e-04, 9.0371184948679912e-04,
    2.4699125636645672e-04, 5.9147458541551113e-04, 3.8444740537595942e-04,
    8.5932297611334600e-04, 6.0598617290751988e-04, 1.4705149603278306e-04,
    1.4431522344877262e-03, 4.5696999458730438e-04
  ],
  [
    2.2806166994472367e-03, 8.7747376727426759e-04, 6.2771773800865524e-04,
    6.1360733950558593e-04, 1.0187249201952210e-03, 6.2154432511249121e-04,
    8.6556272233095357e-04, 7.9279793619671047e-04, 3.8185691425617459e-04,
    2.4545975084797667e-02, 1.0187721075530867e-02, 1.0015355309232945e-03,
    2.3855654456497641e-03, 2.3760161494061206e-03, 6.6596344099825570e-04,
    1.2754928334842836e-03, 2.1146482135048364e-03, 2.8885067061466341e-04,
    1.1275668044226116e-03, 1.2010991497586472e-02
  ],
  [
    3.1400426239163565e-03, 1.5563382766215293e-03, 9.0162895039764071e-04,
    8.9746213145538078e-04, 1.2204913461061227e-03, 1.2200582014470405e-03,
    1.2693446983220930e-03, 1.4084669216931525e-03, 6.9827301155994540e-04,
    1.0187721075530867e-02, 4.7314665506091480e-02, 1.6493087064879096e-03,
    4.9150964217477052e-03, 4.7389371254676835e-03, 1.0204208998598171e-03,
    1.9093387711173759e-03, 2.5387072113370619e-03, 5.5567682513643440e-04,
    1.7591338828767365e-03, 8.0719383241327648e-03
  ],
  [
    2.5717145234657262e-03, 5.6726070720652388e-03, 1.9751605656395136e-03,
    1.7935339070485811e-03, 3.4081454298601579e-04, 2.6612615004061048e-03,
    3.1728712431242272e-03, 1.8091800840455807e-03, 9.0371184948679912e-04,
    1.0015355309232945e-03, 1.6493087064879096e-03, 2.1110006225715187e-02,
    6.5644301788968489e-04, 6.8011754565553524e-04, 1.1433484348853926e-03,
    2.2696044144588988e-03, 1.8742456882945837e-03, 1.4351856033992664e-04,
    6.5878172544710722e-04, 1.2879210940900179e-03
  ],
  [
    9.7190459199705012e-04, 5.5601248568691477e-04, 3.4437514139917542e-04,
    2.8515554540729039e-04, 3.0855994042178013e-04, 6.9614541817054399e-04,
    4.8675933771578960e-04, 4.5905141534639837e-04, 2.4699125636645672e-04,
    2.3855654456497641e-03, 4.9150964217477052e-03, 6.5644301788968489e-04,
    6.7525741637165784e-03, 9.2071349348378116e-04, 2.9821836819244002e-04,
    6.2250823423415716e-04, 8.5497291624530018e-04, 1.8480270544289832e-04,
    4.1789997362558619e-04, 2.0390401916086623e-03
  ],
  [
    1.1707482997247202e-03, 6.0014287440373390e-04, 4.5695294787233016e-04,
    4.9706948686116547e-04, 5.4061743869703049e-04, 4.3847028249800182e-04,
    5.2592632830518644e-04, 7.2640563736237702e-04, 5.9147458541551113e-04,
    2.3760161494061206e-03, 4.7389371254676835e-03, 6.8011754565553524e-04,
    9.2071349348378116e-04, 2.2759929778368840e-02, 3.8203945097730409e-04,
    9.0070409285055049e-04, 9.3733303528124379e-04, 7.0215975437974915e-04,
    4.5967694652672827e-03, 1.9728777259904423e-03
  ],
  [
    1.9972723941546994e-03, 7.7860213318230740e-04, 5.6210182826678802e-04,
    8.3650620447870902e-04, 2.6341296370767072e-04, 6.3169039064483155e-04,
    1.1283633992741310e-03, 9.1606958049118977e-04, 3.8444740537595942e-04,
    6.6596344099825570e-04, 1.0204208998598171e-03, 1.1433484348853926e-03,
    2.9821836819244002e-04, 3.8203945097730409e-04, 2.4044365492630580e-02,
    1.3333728667143045e-03, 9.5861529112551574e-04, 1.0367126137135345e-04,
    2.9369391163915916e-04, 9.1754627765824664e-04
  ],
  [
    6.1234827650497045e-03, 1.7926007027022699e-03, 2.6415583911000790e-03,
    2.1902661040309438e-03, 9.0081780182465609e-04, 1.5347331351459369e-03,
    2.4358395159902540e-03, 3.2250721573096343e-03, 8.5932297611334600e-04,
    1.2754928334842836e-03, 1.9093387711173759e-03, 2.2696044144588988e-03,
    6.2250823423415716e-04, 9.0070409285055049e-04, 1.3333728667143045e-03,
    2.0222291957641345e-02, 4.8820444720790194e-03, 2.0564914018856946e-04,
    8.5252084753556067e-04, 1.9182160488867347e-03
  ],
  [
    3.4990592936902896e-03, 1.3337993839260983e-03, 1.8096241176560255e-03,
    1.4770487412630099e-03, 8.3760722742725604e-04, 1.1633090191045159e-03,
    1.7460695145653721e-03, 1.6376154647606311e-03, 6.0598617290751988e-04,
    2.1146482135048364e-03, 2.5387072113370619e-03, 1.8742456882945837e-03,
    8.5497291624530018e-04, 9.3733303528124379e-04, 9.5861529112551574e-04,
    4.8820444720790194e-03, 1.9324325014986026e-02, 1.8008131088087498e-04,
    7.7364223266285920e-04, 3.0481291734621883e-03
  ],
  [
    3.1628263576966828e-04, 1.8822355540425045e-04, 1.1361193219385239e-04,
    9.6154148977656466e-05, 1.1402385673074935e-04, 1.8118969468635933e-04,
    1.7186658965667723e-04, 2.8505580568873712e-04, 1.4705149603278306e-04,
    2.8885067061466341e-04, 5.5567682513643440e-04, 1.4351856033992664e-04,
    1.8480270544289832e-04, 7.0215975437974915e-04, 1.0367126137135345e-04,
    2.0564914018856946e-04, 1.8008131088087498e-04, 1.0080756092360078e-02,
    9.7237191290610822e-04, 3.3849359263814259e-04
  ],
  [
    9.5781456962094815e-04, 6.3568077704304765e-04, 5.3166878528705414e-04,
    4.1238640135342840e-04, 3.0875531409262481e-04, 4.8090269093961543e-04,
    5.3762929629223334e-04, 5.3377971995623207e-04, 1.4431522344877262e-03,
    1.1275668044226116e-03, 1.7591338828767365e-03, 6.5878172544710722e-04,
    4.1789997362558619e-04, 4.5967694652672827e-03, 2.9369391163915916e-04,
    8.5252084753556067e-04, 7.7364223266285920e-04, 9.7237191290610822e-04,
    1.7299655473877330e-02, 1.0599282277832859e-03
  ],
  [
    4.2309560726043610e-03, 1.1439035919666126e-03, 7.8744578895086331e-04,
    8.1983005205147035e-04, 1.2790175783090351e-03, 8.6038475380201306e-04,
    1.3537458445130380e-03, 1.1777891482397749e-03, 4.5696999458730438e-04,
    1.2010991497586472e-02, 8.0719383241327648e-03, 1.2879210940900179e-03,
    2.0390401916086623e-03, 1.9728777259904423e-03, 9.1754627765824664e-04,
    1.9182160488867347e-03, 3.0481291734621883e-03, 3.3849359263814259e-04,
    1.0599282277832859e-03, 2.8697002670368957e-02
  ]
]