Module xi_covutils.matrices.blosum_45

Background and joint amino acid substitution frequencies used to calculate BLOSUM45 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
BLOSUM45 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_45_BG = [
  7.8254696826829992e-02, 5.2293400508515497e-02, 4.1869234505207159e-02,
  4.9715478669430609e-02, 2.3504091554598174e-02, 3.5913319135963809e-02,
  5.8088865918176615e-02, 7.4985562582061308e-02, 2.4796120028184831e-02,
  6.1906885653760506e-02, 9.3758807045384390e-02, 6.0002347578480664e-02,
  2.5078218042817218e-02, 4.6429254925009635e-02, 4.2599362265185327e-02,
  6.1179450532953900e-02, 5.2495886521295561e-02, 1.3367812099806363e-02,
  3.3781387194819178e-02, 6.9979818411519248e-02
]

BLOSUM_45_JOINT = [
  [
    1.8067859192199651e-02, 2.8632970280029189e-03, 2.5852716092104864e-03,
    2.6802872542729885e-03, 1.4721761726112878e-03, 2.4357016851740214e-03,
    3.7509741193044975e-03, 6.3392371060867767e-03, 1.2691974410907309e-03,
    3.6179059863255059e-03, 5.2267067349121834e-03, 3.6916191127573101e-03,
    1.6118871872377726e-03, 2.1340510849853227e-03, 2.3620871424910785e-03,
    6.2253573100243412e-03, 4.1104541288450981e-03, 5.9150588019808183e-04,
    1.6885104821419373e-03, 5.5306101689579796e-03
  ],
  [
    2.8632970280029189e-03, 1.2981201352308378e-02, 1.9658257815459023e-03,
    2.0049066095474076e-03, 5.7991132007379289e-04, 2.4961427104605001e-03,
    3.0703156814048727e-03, 2.2360083825481514e-03, 1.2617224002813071e-03,
    1.5810689324881372e-03, 2.9473459585734607e-03, 6.0953893700066292e-03,
    1.0175430650195330e-03, 1.4313644854523438e-03, 1.2956809668774457e-03,
    2.5563801601305607e-03, 1.9632608045077912e-03, 4.0556397557578358e-04,
    1.4263902102458958e-03, 2.1140813134646885e-03
  ],
  [
    2.5852716092104864e-03, 1.9658257815459023e-03, 7.8501470034711886e-03,
    3.1259558053206788e-03, 6.6941554412093584e-04, 1.5524817804651980e-03,
    2.1724722312522963e-03, 3.3237456813136586e-03, 1.2666696726132058e-03,
    1.4625067095661482e-03, 1.8988677499765833e-03, 2.8106528553236663e-03,
    7.1583261905988334e-04, 1.1127971670944336e-03, 1.1422087671867729e-03,
    3.0730446623880589e-03, 2.4501354524355920e-03, 2.1811180797041274e-04,
    8.5687995159461643e-04, 1.6162116532974411e-03
  ],
  [
    2.6802872542729885e-03, 2.0049066095474076e-03, 3.1259558053206788e-03,
    1.3237563732845571e-02, 6.2265374552703391e-04, 1.7098653558570117e-03,
    4.7436012699642992e-03, 2.7602948240886133e-03, 1.2034182798676748e-03,
    1.3552305161392132e-03, 2.1559462215056625e-03, 2.8090778444402500e-03,
    6.1643397738889020e-04, 9.9489940177469407e-04, 1.5334105263610980e-03,
    2.8268709927001139e-03, 2.2865632447178858e-03, 2.4814784831918892e-04,
    1.0831280925706914e-03, 1.7172231262216453e-03
  ],
  [
    1.4721761726112878e-03, 5.7991132007379289e-04, 6.6941554412093584e-04,
    6.2265374552703391e-04, 9.4412874076739879e-03, 4.1042025902182758e-04,
    7.4458585782220040e-04, 9.8139056130103924e-04, 2.8594866937112776e-04,
    7.8981156978924646e-04, 1.4823588205010103e-03, 7.7106114710675307e-04,
    3.5586318613686682e-04, 6.5657489327527010e-04, 4.1203914885321426e-04,
    1.1459765491404468e-03, 1.0139516933242551e-03, 1.0481557906271918e-04,
    3.8818429938079952e-04, 1.1756651305043552e-03
  ],
  [
    2.4357016851740214e-03, 2.4961427104605001e-03, 1.5524817804651980e-03,
    1.7098653558570117e-03, 4.1042025902182758e-04, 5.6843729268296912e-03,
    3.1938622849651262e-03, 1.8500970336630773e-03, 1.0245276847880554e-03,
    1.2849197264462630e-03, 2.1618326111720785e-03, 2.8660992672576535e-03,
    8.4702447612542125e-04, 7.3960293189886505e-04, 1.0946565407497567e-03,
    2.3989430846357322e-03, 1.4716698819858265e-03, 3.0973861280282215e-04,
    1.0059662375582828e-03, 1.3753940441066036e-03
  ],
  [
    3.7509741193044975e-03, 3.0703156814048727e-03, 2.1724722312522963e-03,
    4.7436012699642992e-03, 7.4458585782220040e-04, 3.1938622849651262e-03,
    1.3069658477215567e-02, 2.5107356320500625e-03, 1.3852382529276910e-03,
    1.7450831790645173e-03, 3.1086857110181228e-03, 4.4504838476236725e-03,
    8.9571496470550454e-04, 1.3425662787911086e-03, 2.2536863740022671e-03,
    3.2415108480856065e-03, 2.5397857261280324e-03, 4.0327648497408492e-04,
    1.2098752538504236e-03, 2.2567534430266742e-03
  ],
  [
    6.3392371060867767e-03, 2.2360083825481514e-03, 3.3237456813136586e-03,
    2.7602948240886133e-03, 9.8139056130103924e-04, 1.8500970336630773e-03,
    2.5107356320500625e-03, 2.8511624448995753e-02, 1.2310524422167546e-03,
    1.9327062043969442e-03, 3.1643945035180797e-03, 3.0499894759105127e-03,
    1.0995162153881082e-03, 1.6723363525115967e-03, 2.2429535327172330e-03,
    4.8536849682850143e-03, 2.7272360099530155e-03, 5.9271120428223316e-04,
    1.3911803421160626e-03, 2.5146676607186078e-03
  ],
  [
    1.2691974410907309e-03, 1.2617224002813071e-03, 1.2666696726132058e-03,
    1.2034182798676748e-03, 2.8594866937112776e-04, 1.0245276847880554e-03,
    1.3852382529276910e-03, 1.2310524422167546e-03, 5.8487547639124796e-03,
    6.9585846800609714e-04, 1.5573467613102150e-03, 1.3245694120032801e-03,
    5.7090651699323862e-04, 7.8182832078834081e-04, 6.9844962409397991e-04,
    1.2960325177514280e-03, 9.1931607877249958e-04, 1.4976351019639964e-04,
    1.2330522291934879e-03, 7.9246698200683503e-04
  ],
  [
    3.6179059863255059e-03, 1.5810689324881372e-03, 1.4625067095661482e-03,
    1.3552305161392132e-03, 7.8981156978924646e-04, 1.2849197264462630e-03,
    1.7450831790645173e-03, 1.9327062043969442e-03, 6.9585846800609714e-04,
    1.2388694439401509e-02, 9.2647566985432136e-03, 1.9773203824746490e-03,
    2.2593292403687306e-03, 3.0575457844642532e-03, 1.6077385068018789e-03,
    2.3421848303183976e-03, 2.7542711781141610e-03, 4.6749463838911354e-04,
    1.8956764459114616e-03, 9.4267822167510788e-03
  ],
  [
    5.2267067349121834e-03, 2.9473459585734607e-03, 1.8988677499765833e-03,
    2.1559462215056625e-03, 1.4823588205010103e-03, 2.1618326111720785e-03,
    3.1086857110181228e-03, 3.1643945035180797e-03, 1.5573467613102150e-03,
    9.2647566985432136e-03, 2.6346530417480200e-02, 3.1142098082328640e-03,
    4.0711638827261041e-03, 5.6719761997807835e-03, 1.9088185348168649e-03,
    3.1873279813785520e-03, 3.8426846085017905e-03, 8.4082046153240706e-04,
    3.0567323782711214e-03, 8.7503010016331175e-03
  ],
  [
    3.6916191127573101e-03, 6.0953893700066292e-03, 2.8106528553236663e-03,
    2.8090778444402500e-03, 7.7106114710675307e-04, 2.8660992672576535e-03,
    4.4504838476236725e-03, 3.0499894759105127e-03, 1.3245694120032801e-03,
    1.9773203824746490e-03, 3.1142098082328640e-03, 1.1978396089560937e-02,
    1.1104403771137466e-03, 1.4742483750212233e-03, 1.9968025222690676e-03,
    3.2668812435946099e-03, 2.7862613227875948e-03, 4.5043772800615431e-04,
    1.4940888302424689e-03, 2.4843185667476147e-03
  ],
  [
    1.6118871872377726e-03, 1.0175430650195330e-03, 7.1583261905988334e-04,
    6.1643397738889020e-04, 3.5586318613686682e-04, 8.4702447612542125e-04,
    8.9571496470550454e-04, 1.0995162153881082e-03, 5.7090651699323862e-04,
    2.2593292403687306e-03, 4.0711638827261041e-03, 1.1104403771137466e-03,
    2.5874360305861857e-03, 1.2371987255888946e-03, 6.8765677463444332e-04,
    1.0131873446874034e-03, 1.1327846844696357e-03, 2.1265849704555571e-04,
    8.6680034269080448e-04, 2.1688399348504966e-03
  ],
  [
    2.1340510849853227e-03, 1.4313644854523438e-03, 1.1127971670944336e-03,
    9.9489940177469407e-04, 6.5657489327527010e-04, 7.3960293189886505e-04,
    1.3425662787911086e-03, 1.6723363525115967e-03, 7.8182832078834081e-04,
    3.0575457844642532e-03, 5.6719761997807835e-03, 1.4742483750212233e-03,
    1.2371987255888946e-03, 1.2391203870190888e-02, 8.9236221263296761e-04,
    1.7312816295078565e-03, 1.7453918151105632e-03, 8.4095245274993082e-04,
    3.4263744717066835e-03, 3.0946984716836139e-03
  ],
  [
    2.3620871424910785e-03, 1.2956809668774457e-03, 1.1422087671867729e-03,
    1.5334105263610980e-03, 4.1203914885321426e-04, 1.0946565407497567e-03,
    2.2536863740022671e-03, 2.2429535327172330e-03, 6.9844962409397991e-04,
    1.6077385068018789e-03, 1.9088185348168649e-03, 1.9968025222690676e-03,
    6.8765677463444332e-04, 8.9236221263296761e-04, 1.6004098119159461e-02,
    1.9539606804874826e-03, 1.9148086102650892e-03, 2.9896951765680344e-04,
    6.8907122080648483e-04, 1.6099029423219423e-03
  ],
  [
    6.2253573100243412e-03, 2.5563801601305607e-03, 3.0730446623880589e-03,
    2.8268709927001139e-03, 1.1459765491404468e-03, 2.3989430846357322e-03,
    3.2415108480856065e-03, 4.8536849682850143e-03, 1.2960325177514280e-03,
    2.3421848303183976e-03, 3.1873279813785520e-03, 3.2668812435946099e-03,
    1.0131873446874034e-03, 1.7312816295078565e-03, 1.9539606804874826e-03,
    1.0412392255159685e-02, 4.7291383160678064e-03, 3.5033107367116276e-04,
    1.4588588725561497e-03, 3.1161052123834937e-03
  ],
  [
    4.1104541288450981e-03, 1.9632608045077912e-03, 2.4501354524355920e-03,
    2.2865632447178858e-03, 1.0139516933242551e-03, 1.4716698819858265e-03,
    2.5397857261280324e-03, 2.7272360099530155e-03, 9.1931607877249958e-04,
    2.7542711781141610e-03, 3.8426846085017905e-03, 2.7862613227875948e-03,
    1.1327846844696357e-03, 1.7453918151105632e-03, 1.9148086102650892e-03,
    4.7291383160678064e-03, 8.6497284024982021e-03, 3.1868671219664247e-04,
    1.3184355271303671e-03, 3.8213223234837145e-03
  ],
  [
    5.9150588019808183e-04, 4.0556397557578358e-04, 2.1811180797041274e-04,
    2.4814784831918892e-04, 1.0481557906271918e-04, 3.0973861280282215e-04,
    4.0327648497408492e-04, 5.9271120428223316e-04, 1.4976351019639964e-04,
    4.6749463838911354e-04, 8.4082046153240706e-04, 4.5043772800615431e-04,
    2.1265849704555571e-04, 8.4095245274993082e-04, 2.9896951765680344e-04,
    3.5033107367116276e-04, 3.1868671219664247e-04, 5.3077625858668461e-03,
    8.1328347217338593e-04, 4.4278005713663357e-04
  ],
  [
    1.6885104821419373e-03, 1.4263902102458958e-03, 8.5687995159461643e-04,
    1.0831280925706914e-03, 3.8818429938079952e-04, 1.0059662375582828e-03,
    1.2098752538504236e-03, 1.3911803421160626e-03, 1.2330522291934879e-03,
    1.8956764459114616e-03, 3.0567323782711214e-03, 1.4940888302424689e-03,
    8.6680034269080448e-04, 3.4263744717066835e-03, 6.8907122080648483e-04,
    1.4588588725561497e-03, 1.3184355271303671e-03, 8.1328347217338593e-04,
    6.5658130332894053e-03, 1.9130855013886519e-03
  ],
  [
    5.5306101689579796e-03, 2.1140813134646885e-03, 1.6162116532974411e-03,
    1.7172231262216453e-03, 1.1756651305043552e-03, 1.3753940441066036e-03,
    2.2567534430266742e-03, 2.5146676607186078e-03, 7.9246698200683503e-04,
    9.4267822167510788e-03, 8.7503010016331175e-03, 2.4843185667476147e-03,
    2.1688399348504966e-03, 3.0946984716836139e-03, 1.6099029423219423e-03,
    3.1161052123834937e-03, 3.8213223234837145e-03, 4.4278005713663357e-04,
    1.9130855013886519e-03, 1.4058608660834061e-02
  ]
]